Skill Focus isn't the same thing as giving you additional skill points. You are limited to a maximum of (level +3) points in any skill that is a class skill, and a maximum of ((level +3)/2) in any skill that is a cross-class skill. Aside from item/spell bumps and your stat modifier for a skill, the only way to persistently increase a skill above and beyond this is to take Skill Focus. This grants you a +3 bonus to one skill, with no regard to the maximum ranks you can have in a skill.
Take, for example, everyone's favorite - UMD. If you have a 1st - level bard or rogue, maximum ranks at 1st level are 4. With an 18 charisma, your total skill check is going to be 8. The same Bard or Rogue with Skill Focus (UMD) would have a total skill check of 11. Your other skills are unaffected, and you still can't put more ranks in UMD than level+3, but you get to add a +3 bonus on top of that.
Adding skill points doesn't change the maximums of class or cross-class skills, it just lets you broaden your character's knowledge a little bit.
As far as the AP/Feat balance, insomuch as the AP Enhancements have essentially replaced prestige classes, and to a lesser extent cleric domains, I don't think they're too powerful. I wouldn't hand out a whole bunch for a feat; something like 2 seems balanced. Trading an inherent extraordinary ability you get every three levels for something you get every two levels otherwise doesn't sound particularly overpowering to me.
And, btw, just because some of us have dragonmarks, it doesn't mean we have 'feats to burn'. Not all of us who play this game are zerging min-maxers.