I'd want another Unearthed Arcana type book, full of setting-free *options.*
I'd want to take the best ideas from Monte Cook's Arcana Unearthed, such as the magic system, and the best ideas from Iron Heroes, and strap them together to revitalize the magic using and melee combat classes.
Metamagic feats and the Tome of Battle stuff would die a tragic death. The arcane / divine caster split would likewise die. If I want to run a D&D game without religion, I shouldn't be limited to Bards for healing magic... If I want to run it with a horde of divinely-sponsored casters, or make *all* casters divinely sponsored, that too should be an *option,* not a hard-and-fast straightjacket.
Prestige Classes would die. Far too setting-specific. Any PrC class ability worth having would be part of a Feat chain, or an Alternate Class Feature for one of the base classes. Specialized core classes would similarly die, with the Barbarian, Ranger and Monk all being reduced to Feat Chains that a Fighter can take, to turn himself into a near-exact duplicate of the current Core Monk, Barbarian or Ranger, or mix-and-match to a limited extent, to be a light skirmishing Fighter with Rangery dual-wielding, a Barbarian's Rage and a Monk's unarmed AC and movement bonus, for instance. If my 'lawful' martial artist wants to be able to enter a focused state of combat zen / moving meditation that functions mechanically as a Barbarian's Rage, he should be able to buy the Feat chain to do so, without being artificially constrained by 'alignment' concerns or 'monks can't cross-class' concerns or any other setting-specific crap.
Magic would be set down as a list of 'effects,' with multiple systems for achieving those effects. One would be Vancian fire-and-forget. One would be a spontaneous casting mechanic. One would be a mix-and-match Ars Magica / Mage: the Ascension / True Sorcery / Freeform style. One would be spell points. Pick the flavor most applicable to your own style, or even have multiple mechanics in the same world (as D&D already does with Sorcerers and Wizards and Psions). Yeah, I included Psionics there too. As far as I'm concerned, it's just another form of 'magic,' in that it's a system arranged around doing 'other stuff.' Call it mental powers, call it arcane might, call it 'invoking divine favor,' call it mutant goat-cheese for all I care, it doesn't need *an entirely seperate set of rules* to do the same darn things. *One* list of effects, whether you cast spontaneously, prepared or freeform and whether or not you call your 'special fantasy power' magic, psionics, incarnum or the-art-of-flipping-out-and-killing-stuff. These rules would be completely setting independent. A 'spell' (power) that allows you to channel all of your 'magical' potential (psychic discipline, whatever) into melee combat wouldn't be called 'Tenser's Transformation,' it would be called something like 'Warrior Mind,' with a note at the bottom that spellcasters in the Greyhawk setting call it 'Tenser's Transformation' after a particularly militant spellcaster of that setting. Effects would all scale, like Fireball or Summon Monster, increasing with a) higher level spell slots, b) more spell points blown, c) greater strain on the caster, d) whatever. Similarly, a higher level caster could cast a 'diminished' version, to save power, or when he's scraping bottom of the spell point pool / slots per day.
I'd 'normalize' the monsters vs the PC races. No more bizarrely assigned stats, leading to a stableboy getting killed by a Ghoul and rising with a higher Charisma score than the King. The *biggest* problem with the notion of Savage Species was the ridiculous and inconsistent levels of various attributes and abilities possessed by many of the beasties in the SRD. Monsters with 'casts spells as an X level whatever' would lose those features and simply be listed as 'blah-blah Eladrin are *always* at least 7th level Clerics, with two of the following Domains.' I hate one set of rules for PCs and another for NPCs. *One* set of rules. Then, when someone *inevitably* wants to play an Aranea or something, there doesn't have to be a lot of hands-waving and running about trying to kludge a fit between things that *weren't properly designed according to the same rules.*
The Spiked Chain would die. I will happily suspend disbelief to include multi-tonned 'cold-breathing' arctic flying reptilians, but that piece of crap spits on the laws of physics and jumps up and down on the grave of common sense, and doesn't even have the excuse of being magical to hide behind.
Vermin would gain Intelligence scores. Bees are as trainable as rats. Bees the size of ponies that can be trained to serve as flying mounts? Yeah, definite Intelligence score and *not* immune to mind-affecting effects. Try again. Same for any other thing with an Intelligence score. If that Treant can talk to me, if that Ooze can cast spells, then they've got minds to 'affect.' Stop with the random granting of immunities (or sense types) that make no sense (such as those sightless underdark critters who happen to get free Darkvision as part of their 'type').
The Swarm rules suck. I have no brilliant idea how to fix them, only that their current implementation mocks my delicate sensibilities.