Scaling Feats
Scaling depends entirely on how the feat accomplishes that - a feat that grants a +1 bonus to say, Bluff, each level is radically more powerful beyond level 3 than Skill Focus (Bluff), and rapidly begins to get silly beyond that - and that's all ignoring Skill Focus is generally bad for most characters and builds. But a feat that grants +2 to Bluff for every 5 character levels you possess isn't really an issue to me by comparison because its still radically eclipsed by everything else in the game by the time that +8 at level 20 comes around, or even that +4 at level 10.
I suppose the best example I can think of is the non-existent scaling of mundane bonuses, such as the +1 to attack, +2 to damage, etc - they can't, and never will scale simply because that feat is a 1 for 1 trade, or 1 for 2 trade; you only, forever, get that +1 to attack (or +2 to damage), rather than a scaling bonus to attack (or damage) every X levels.
They're silly compared to other things like Power Attack which naturally by design scale.
Greater Feats
Greater feats should be greater, as in, you sunk 2 feats to do X, it really should do X better than Y or Z.
Going back to the previous example, which is obviously Weapon Focus (or Weapon Specialization), why is Greater Weapon Focus effectively the same thing as Weapon Focus? Why bother calling it "Greater", aside from the fact it takes Weapon Focus (which doesn't stack) and a higher Fighter level when it does the same thing as Weapon Focus but stacks the benefits, for a pitiful +2 bonus to attack rolls? Why doesn't it provide something like a +3 bonus to attack rolls, which explicitly stacks with Weapon Focus? Its "Greater" after all.
In general, I have no issue with the concept of "Greater" feats, except for their application - they should be much improved versions of the feat before hand, not more minor, effectively non-existent increments.
Feats with Per Day Limits
Again, my issue is application. Most of these "uses per day" suck, or don't make significant enough impact to really validate themselves, especially when they're used in conjunction with something your character does all the time anyway... unless it opens up a new feature to your character, a talent they couldn't usually preform, and is relatively a large change to the standards of the character (Fighter getting a feat that has a 1/day SLA that provides say, Fly).
Most of these "Per Day" feats should be per encounter/combat - their benefits are marginal, useful at times, but not ground breaking enough to merit only X amount of uses per day.
