In general, 3.0e was superior to 3.5e.
But this doesn't mean that 3.0e was without problems. There are a lot of things to take care of and what you take care of is a personal preference.
At the minimum I would recommend people who stick with 3.0e:
a) Ban PrCs. There is a long discussion why but PrC's break 3.0e's design in multiple ways and were kludged into being the solution for multiple problems and oversights with 3e D&D's design (multi-classing casters and non-casters for example) in ways that ultimately were unhappy solutions.
b) Evaluate the version of the spell in 3.0e and 3.5e and always take the weaker version of the spell. 3.5 broke the game with a bunch of unneeded spell rebalancing - the fixes to haste and harm were offset by breaking so many other spells. Avoid adding a lot of new spells to the game that solve some big problem that casters have, as casters really don't need more solutions.
c) Drop the rule that the level of a spell adds to the DC to save from the spell. This requires a few other rewrites, but it is worth it as this change alone goes a long way to producing parity between casters and non-casters. Additionally, go ahead and drop the rule that half the HD of the monster adds to the DC of saving versus its non-spell abilities. One problem with the 3.X design is that unlike 1e/2e, as the consequences of failing a save increase the chance that the PC succeeds in the save doesn't go up, producing a situation where in order for high level PC's to survive they need magical aid in the form of immunities. And that blows the balance between casters and non-casters completely away. With these changes, save or suck stops being the obvious winning strategy. After banning PrC's you'll probably also have gotten away of a lot of the easy ways to up DC to the point that spells reliably succeed.
d) Ban divine wands. This is a bit more controversial, but divine wands weren't really present in 1e/2e and they create lots of weirdness - most notably with the massive efficiency of Wand of Cure Light Wounds, but really in general.
e) Ban the "Natural Spell" feat. Avoid power ups to the Druid class introduced by 3.5. I banned it entirely, but it's a lengthy discussion of how to ban the class but retain the class concept of an animist spellcaster.
f) Nerf the Cleric slightly by reducing its available spells in each spell level by one. In other words, at some levels it will be 0+1D spell, having access to only it's domain spell. Secondly, require the Cleric to have a spell list similar to the sorcerer so that it does not have access to every divine spell. This avoids the problem of every divine spell you introduce automatically becoming a cleric class feature and along with the above prevents CoDZilla.
g) Redo the fighter by giving it more skill points and more feats. Four skill points and one feat at every level not divisible by 3 up to 15th level and then an extra feat at every level above 15th level works pretty well (so like 2 bonus feats at 16th). It still won't get it up to tier 3 without some more help but it does make fighters relevant.
After that it very much gets to be preference and figuring out what to bring in to add to the core rules that does actually benefit the game.