1st, some feats are just plain boring and are utterly mechanics driven. Skill focus is a pretty uninteresting feat and while say Combat Casting is mechanically useful, it too adds little fun to actual play.. Its more of a resource tax that adds little zing to the table.
Many other feats, combat meta-magic and such in my opinion feats serve more as breaks on what character can do and mostly to doll out the awesome rather than encourage it in abundance.
Let me give you a few examples.
Feat Chain #1
In 3x , roughly this feat lets you take another attack if you drop a creature in a given round. Once. That is if you have the prerequisite buy in.
Following up after this is Great Cleave (like Cleave but several times a round) and in various supplements and house rules a whole chain (Supreme Cleave lets you take a 5 foot step and even seen Trail of Blood letting you use your full move)
This is good and fine but why not simply give this all fighters thusly ..
Any time a Fighter (maybe of of L3 and up if you like) drops a foe, he may take a free swing on any foe within his reach up to his move.
This is roughly equal to giving a fighter the entire Cleave feat chain (including the variants) but so what? Unless the character is fighting a horde of minions or something (which in many editions gets him 1 attack per level!) all it does is give him a chance to shine every so many battles which is a fine thing.
Now a fully concede that feats do allow any class (even a Wizard if thats what you want) that has the stats to do this things, and in game where there is some erosion of niche protection this can be a good thing. However its not that hard to do for other games, either with a small XP hit as a custom class (for the Thief , the Ranger or whatever) or with some kind of Gift system.
let me show you another chain,
Feat Chain #2 Spring Attack
This chain requires 2 prerequisites (Dodge and Mobility) and basically allows a person to attack once at any point in their move. Later feats in the 3.5 Players Handbook 2 allow extra attacks to be taken with some penalties.
I have two word for that. Complicated & Boring. As I see it, mobile combat is fun and it makes more sense to allow anyone to moved and attack if they like, especially in older editions where they are unlikely to have a ton of attacks.
The same thing applies to the various feat chains for things like Bull Rush and Disarm and Feint and such which now (as for Ultimate Combat which I saw a peak at while it was under construction and up on the PFSRD) has chains to allow you the privilege of making one of yor attacks a trick or bull rush or something . As I said Boring.
Instead of limiting these things, once you have a good rule you ought to encourage more of them. Rather than static combat or move into combat than attack, why not have mobile swashbuckling battles with thrown cloaks and slams and grapples and shoves and more
If extra attacks by weapon specialists or two weapon fighters are an issue, just jot down a note like.
Weapon Specialists and Two weapon Fighters gain extra attacks with various weapons. Such attacks may only be used to attack
Simple concise, clear.
And yes the same things apply to creating magic items (any caster of the appropriate level should be able to do it) and if fitting Metamagic feats. I mean really, if you want say maximized spells in your game just make them use a slot 3 levels higher. Quickened spells, 4 levels higher and so on.
Doing this will allow a lot more variety and is still resource limited by either ones to hit bonus or spell slots thus preserving balance.