No feat or PrC should have more than one feat-based prerequisite, unless it combines two things together. If Greater TWF requires Improved TWF which requires TWF, then that counts as Greater TWF having two prereqs and is bad. Level and skill prereqs are okay, though the latter should also be minimal. Granted, this approach would remove some of the "puzzle" aspect of 3.5e which many find attractive, but also means you don't have to plan your build from lv1.
Feats should be signature abilities. In other words, if a character has a feat then it should be obvious from observation - no feats should just boost your numbers, since that's indistinguishable from being higher level/having higher ability scores (and boring). You should be able to guess a character's feats from hearing bards sing about them (and not in the sense of "he's a barbarian, all barbarians have Power Attack", more "he drank their souls to increase his power" or "he threw his weapon and it ricocheted around the room to hit multiple enemies"). This means fewer PrCs, since feats cover the same ground, but it lets you play PrC concepts from lv1.
Applying metamagic to a spell is done at casting time, and requires expending other prepared spells of equal or higher level (applying a +2 modifier to an lv5 spell would require you to expend either two lv5 spells or an lv6+ spell, in addition to the normal slot), assuming a system more like psionics isn't being used. Silent Spell/Still Spell/Eschew Materials are folded into a single feat called
Simplified Spellcasting, which lets you remove one component from a spell for each additional slot expended.
Possibly all spellcasters work like sorcerers but their spells take a full-round action to cast. In this case a "Spell Preparation" feat exists which functions much like
Arcane Preparation, and lets you cast them as a standard action (or a swift/immediate action, if you use a higher-level slot).