I enjoy F&K primarily because there are not any loaded choices. Aside from the "if you are a Conduit, you must get Heighten Spell-like Ability, there are a very limited number of BAD choices. If you are an assassin demon and take a stinging scorpion tail, that is perfectly fine. If you take Danger Sense, that's cool too because you get to see all the traps instantly.
Seriously, I'm in a campaign with a newbie player playing a Conduit (limited number of spells = good). She has taken Devour the Soul (house-ruled to a full round action), Heighten Spell-like Ability, and Greater Teleport without feeling that she has made a mistake. Also, she can Power Attack with her Flameblade, which I feel is an important addition.
I love the Tome series; it's a shame that there will be no more additions any time soon.
But when Frank and K could have focused on the three other editions, why did he stick with 3rd edition to write about instead of the others? What did he find appealing?
4e was announced after they moved to separate continents. 3rd edition has advantages of rules clarity and flexibility over AD&D. saves make more sense, BAB is understandable by mortals, and there are serious power imbalances. 3rd was also the dominant edition when they started writing.