I'd re-write the whole thing, but I'd make sure to leave enough out so that I could sell version 4.5 a few years later.
Seriously, though, here are some ideas.
I'd include the Leadership feat, or at least enough to give the player more information.
I'd include a magic item section that gave players enough information about things like item slots, and bonus types, so that my players wouldn't have to spend so much time digging through the DMG when they have enough gold to buy an item.
I think I'd like to see the spell system reworked so that two things change. First, some kind of BAB for spell casting is included (Thanee proposed a system elsewhere on these boards and I've adopted a version for my campaign). Second, I'd probably retool all the spells so that the spell levels don't go from 0 to 9, but go from 1 to 20 instead. Further, I'd allow for rules to expand spells from levels 21+ and scrap the Epic spell business.
I'd have two different rogues, one that's combative, as the current rogue seems to be (i.e. uncanny dodge, evasion, sneak attack) and another one that's based around the Charisma ability (bluff, diplomacy, etc.). I don't like that the two are melded together. A solution to this could be to use something similar to the talent trees that are in d20 Modern. Yeah, I like that. I'd bring in the talent trees from d20 Modern.
Oh, I'd probably not stick with 5- and 10-level prestige classes, since so many saves and BAB progressions don't fit well (I like the way that a 6- or 8-level prestige class works better).
I'd introduce the average save progression, it would be a rare class indeed that had two good saves (perhaps just the ranger and monk).
Dave