Here's something that I think will make everyone happy, while not being ridiculously tough to program. It's a system that allows removal of up to two splash levels and alignment changes.
Firstly, you cannot use Greater Reincarnation unless you are at least character level 3.
Upon using Greater Reincarnation, you start as a level 0 character (-1 XP, 20hp, no abilities, all ability scores 8+racial) and transported to a demiplane (like the Portable Hole) with one of each class trainer. All your gear is put in the Reincarnation Bank.
For each class level you had, you are given a token allowing you to level up once in that class at a series of trainers. Upon levelling to 1, you choose your race, then your stat point allocation (using 32 point builds if they are unlocked), and skill point allocation. Don't choose your alignment yet - you'll choose it as the final step, as you leave this demiplane. (Note that as you can only level up in classes you were previously a member of, you cannot create an alignment paradox like a Pal/Brd.)
You cannot leave this demiplane until you have 2 or fewer level up tokens left in your inventory. This prevents players using this to reset to level 1 and totally change their character..
After you finish levelling up to your previous level (or one or two levels lower, if you are doing this to remove a splash), your XP is set to the lowest amount possible to be your new level. (Example: A Wiz17/Rog1 that's only 135 XP short of level 19 goes through this procedure and leaves as a Wiz17, having decided to leave her trapsmithing days behind her. She finishes the proceedure as a level 17 Wizard, with the minimum possible XP to be level 17, and must re-earn the ~1.9 levels worth of XP through questing to return to her old level.) You then select an alignment (from all the alignments possible that do not conflict with your new class level choices), and you are good to go!
*Edit: Tomes apply as they do in the Lamania implementation of Reincarnation - your +2 tome is totally dormant until level 3 and isn't fully effective until level 7. If you have eaten a +2 tome and sacrifice enough levels to fall under level 7, you receive a binds-to-character +2 tome of that type (Min level 7) which sits in your Reincarnation Bank, and a +1 (ML3) tome if needed too.)*
This will allow players to:
1) Remove a splash (such as ClrXXX/Sor1) that may have been good once but is now regretted.
2) Fix alignment issues, allowing people to choose to splash monk, or to safely use that Litany of the Dead trinket they have in the bank
3) Re-order class levels, to allow players that made a mistake such as taking their first level of Rogue at a level other than 1 to correct these mistakes.
4) Change race. The Reincarnation spell in D&D lets you do this (in fact it forces you to).
I have quite a few characters I'd reincarnate this way that I wouldn't use one of the other reincarnations on.