By "fixing 3e", I assume you mean "using the 3e monster manual with new rules for PCs". To avoid re-writing the entire monster manual, because that is BIG JOBS.
In that case, the actual bonuses things get to skills need to be the same, because the monsters have those already.
The
entire skills chapter can go die in a fire though.
+15 Spot should basically be True Sight, and +15 Climb should be running and fighting on the ceiling or clouds or whatever. +15 Diplomacy should be that you can stop the fight music at will and talk instead. +15 Knowledge (Local, aka Carousing, Gather Info, etc) is where you just know everything there is to know, locally, about everyone, but maybe miss the odd special secret thing.
If you're having a skill called Use Rope, you best end up being Wonder Woman, at +15.
And +15 Tumble is where you just ignore attacks of opportunity for moving. If you have +15, the answer is yes you can, even if it's mostly impossible. If Fighters need to fly by 10th level (and they basically do), then Jump +15 needs to be a functional fly speed, even if it costs you a move action.
Most of the skills don't need folded together, but the Knowledge skills do. Obviously, at DC 15, you should also know everything, except for some secrets.
Like, you could give PCs more skills, another couple per level each does sort of help, but think bigger too.
On
Monster Hit Dice not really working for stuff. Again, let's not re-write the entire monster manual, stupid monsters have 2 HD or sometimes 3 HD per CR, and the fact that you can't turn big stupid undead, but instead only little mook undead and the smart ones, is a feature, not a bug. Stab 'em.
Monster hit points are generally a bit big for the sort of damage PCs can do with weapons and damage spells. Don't be afraid to eyeball any monster's hit points, realise how stupid that is, and half it before the battle starts.
The
PC saves are too low, like, by a lot. And not just because dragons have stupid high DCs, so do random NPCs, high level characters should make their saves.
Less changy solution: You need both the cloak of saving throws and another +1/3 level to saves before they can work reliably. To some extent you just use +1/level to all saves for everyone, plus the saves cloak. You can't do that for monsters though, because HD and stuff, so don't.
More changy solution: DC 15. Everything is DC 15, no one gives a fuck what the dragon's Con and HD is, nor how Wise is the Cleric (who already gets more spells from it). +12 Fort basically works all the time even naked and +6 Fort can work most of the time with a modest bonus. Giants, middling Dragons, and big Demons all make all their saves all the time, so select your spells appropriately.
You get way too much
XP awards from level 3 to level 14. That's where the game works, and instead of levelling up every 13 easy fights, you should probably take four to six times that long around the best bits at level 7 to level 10, as everyone did in AD&D. Just change the XP awards by CR by PC level so that they do that, and yes that means you get less XP for a CR 8 monster at level 8 than you did for a CR 3 monster at level 3.
Do not modify the treasure per encounter. PCs also happen to need about 4x as much treasure in the middle levels, and you should give it to them easily here.
Additive
multiclassing is a bad thing and the patches for it amount to hundreds of pages to bring just a few of the possible combinations into functional form.
So, when your 15000 Xp level 6 Fighter decides to go Wizard, just have it cost 1000 XP to get the first level, and then buy Wizard levels like a new character, so that he's level 6 after another 15000 XP, where a single class would be 8th), and when he reaches level 19 the single classes are only level 20 and he doesn't have to be too sad about the Fighter levels still. Keep class totals and swap back and forth as you please.
All your bonuses, attacks, hit points, saves; overlap and do not stack, they're class bonuses. Ditto your feats by level, stat boosts by level, and so on. You've already had a level 6 feat, get to level 9 in any class for your next feat. Record all HD totals by class and use the highest as your maximum.
The numbers, interestingly, come out almost identical to most multiclass patch Prestige Classes, so you can just use the NPCs as written and not even notice.
Also fixes all the playable monsters rules automagically. Overlap and do not stack the class table bonuses and max hit points with the monster's racial bonuses and max hit points. When your class stuff finally gets better, you'll also have level-appropriate powers.
You do just have to give the same XP to everyone in the party to avoid figuring out what level everyone is. Use the highest level PC, NPC, or highest CR monster ally for all XP calculations.
Chuck almost all prestige classes in the bin, if they have any useful abilities, turn them all into a single feat and be done with it. If they are actually an interesting class in themselves, which very few are, write them up as a class, 15 levels or so. You won't do that and no one will care, it's all good, this opens up a huge range of playable characters.
Sadly breaks the thing where you can be a Fighter/Ranger/Barbarian who's slightly better than a Fighter or Ranger or Barbarian. Don't care, and neither do you.
Talking
about Feats. Fighters have 10 of them at 10th level, Wizards 7, and everyone else 4. They need to be really good at that, because firstly it's all Fighters get, and secondly there's too many of the bloody things otherwise.
This has been covered, but in general each chain of 3-5 feats needs to just be a feat. Maybe some things come online later, or they all start immediately, either way is fine. So with Power Attack you can also Sunder, Overrun, and Bullrush. With Combat Mobility you can also Spring Attack and Whirlwind Attack. Mounted Combat is every damn feat that requires it. Still/Silent/Quicken. Whatever, bundle 'em up.
Class features, some of them are very bad. Make them worth knowing.
Pathfinder Smite, for Paladins, that's a smite, it lasts all fight, does solid level-appropriate bonus dice damage, makes people care that it exists.
Trap Sense is terrible, it should do something that matters.
Evasion is good. Sneak Attack is good. Animal Companion is good.
Favoured Enemy needs to be a lot better, like +5d6 damage and a whole new enemy to hit it with, and also 8 categories instead of 33, so that you can just fucking use it.
Iterative attacks, the penalties are stupid. Your off-hand/face/foot attacks are all at -5, or -2 with multiattack(/etc as one feat), your iterative attacks are all at +0. No, there is no penalty for swording while using your "I can kick things" feat to kick things while also using a sword.
Just, in general, melee PCs need to be doing more damage, not less, cheese it up. Missiles it just saves you using touch attacks.
Also, your iterative attacks should be a standard action, or charge, or spring attack. All primary attacks for monsters should be too. Two claws +9, bite +7, that's two claws on a charge. You can use your off-hand extra attacks, shield bashes, or whatever, once you're stuck in combat.
Monks have full BAB, plus extra attacks, with this, OK, also everything else you can imagine to give them, including being a Tiger.
Critical hits are both very uninteresting, and the monsters will kill your character with them if you ever give them picks or even axes.
For the most part, a critical hit chance should be an extra attack that uses the special combat attacks with no touch attack or AoO required. They should only work on your first attack in your action, and can be targeted against a different critter.
Now, when the troll crits you, it's a free trip attack, and combat got more interesting. It's still likely +4 to the next attack and a rend, so yeah, good luck, but less instant-kill from the axes and stuff.
Those x3 and x4 crits, probably need something else if you want to keep the weapons in play, either a bonus to trip/disarm/whatever, or some small damage added to the special attack.
Things that just do double or triple damage, like a lance charge, that's fine, those replace iterative attacks if you use 'em though, mostly good for punching through DR.
But speaking of
special combat tricks, Grappling is awful, most of the rest aren't much better. Who wrote all that shit.
Really. The numbers are both terrible and in the monster manual. So eh, leave 'em. But mechanically ....
Everything should be a touch attack, then the higher roll gets to trip, or sunder, or disarm the lower. No attack of opportunity, they can just win, or not. Both down on a tie. In the case of a grapple, you're either both free if the defender wins or both grappled otherwise.
See also touch attacks, because those are also stupid.
Touch attacks you say? Bad! No you can't just cast Harm on high level things like that, what a stupid fucking mechanic.
But, there's another mechanic that uses the right modifiers anyway, the Reflex save! Any time a touch attack is called for, use a Ref save instead. DC 15 if using all DC 15 saves, or 10 + half HD + Dex otherwise.
Collectively, this handily makes high level characters and monsters mostly immune to being tripped or disarmed, except on 1st attack crits or special automatic trip/grap/etc monsters. You could also allow them a Ref save to mostly avoid that particular automatic brand of bullshit and make the Freedom of Movement thing less compulsory, especially noting that the trip feat is just free with all the other expertise/disarm/whatever ones, and not your entire character concept.
Residuum of a sort. It's good for the game, mechanically if not in concept. When you have magic items you don't want, either swap 'em for other randomly generated magic items at the shop, or build your own with your feats and use those as the component cost.
Note that as you get no more magic treasure for burning it, and treasure needs hacked to bring it higher, you can always turn 1000 gp of magic you don't want into 1000 gp of magic you do want, OK. So if you need a submarine for a while, just make one out of excess swords, and that cloak you're not using right now, and get the cloak back later by burning the sub. It's fine, just uses downtime and a touch of XP or whatever.
Personally I'd say magic is all runestones and gems and embedded eye of beholder, so when you break it down you have a nice masterwork sword and all the magic components to work into other stuff, nothing is actually burnt to magic dust, but the cost and replacement thing is nice and more appropriate than shopping.
The shops are all randomised. All of 'em. Always.
XP costs are ... well, they make sense in world and suck for PCs. Same for level drain. In general, the old AD&D fix was a good one.
When drained, you have max XP (your original total), and current XP. When gaining XP, you gain max XP and gain double current XP until they match. Effectively the long-term cost is nothing, but it still limits how much you can spend on a per-adventure basis.
If your current XP is down a level, use the negative levels mechanic. Never actually lose a level, even with level drain, that's overly punative. This limits item creation and hurts short term with drains, you just catch up.
Some
specific spells are also somewhat problematic for the game in general.
- Polymorph (Other and Polymorph Self), please see 2nd edition versions. Basically, if you get turned into a Troll, use the MM entry only, also go insane and lose the character after a while. If the Wizard turns himself into a Troll, use the Movement rates, skills, and senses of the Troll only.
- Alter Self lets you become a Humanoid, no matter what you are. All those monster manual entries with weird polymorph (but only to a Humanoid form), they have Alter Self.
- Gate is less bad if he takes a share of XP and ups your level for XP calculations, and they are self willed, barely sane, and will want to murder you if you mess with them.
- Planar Binding ditto, just, be cool, work with the desires of the monsters. Angels will help you defeat demons, and take a share of the XP. Efreeti might murder you for your insolence, but also totally make a fair deal that they stick to, figure out what it wants, maybe use your +15 to Arcana.
- Wish is a little off, in general, but rule of thumb, if you wish for anything that could possibly get you another wish, or any other stupid loop, it will monkey-paw your ass so quick. But if it's just a one-off, you get what you want, it's fine.
See also touch attacks, PC saves, a lot of things are much less "lost initiative? game-over!", especially in concept and planning, if they work a lot less reliably.