I also like the idea of trading skill points and feats, as long as you can't build instant feat chains a character of low level should not normally be able to have because that could cause headaches; 25 points for one feat might cover that anyhow but I haven't done the math. The Skill Focus feat doesn't look like a good trade, though
Why the need to have different costs by class level? To me (and the following text is all IMO) the game is making an assumption about what's going on during training, and budgets the time out for you:
- the rogue is devoting a bit of time to improving his combat ability (BAB and HP), but spends much more time practising skills. He does NOT get more skill points because he is any better at learning necessarily, he gets more points because he's devoting a lot of time to it.
- the cleric spends the same amount of time improving his offense abilities as the rogue does (same BAB progression), and a little more to defense (higher hit die) but devotes much time to praying for higher-level spells, more power over the undead, or whatever it is clerics do in your campaign world to improve their divine abilities. They only have a bit of time left over to work on their skills.
- Wizards and sorcerers spend so much time honing their arcane power that they spend very little time improving combat OR skills.
Interpreted this way, what goodies you get on your next level jump would depend on how you budgeted your time. The default game handles this for you in a logical way, but I don't see why the rogue should get extra-punished for cutting down on his skills training to free up a big gap in his training time, and practising something else in that frame instead. He's already giving up the ability to be a complete master of the standard "rogue stuff", kind of like multiclassing.
This idea might be completely messed-up if applied to the house rule actually at hand in this thread, I don't know. You can probably tell by now that I'm a point-buy kind of guy.
