I will also engage in blasphemy, but go even further -- instead of "prestige classes" why not a "class replacement" option that allows a character to take the abilities of another class as its "level." This would be after 5th level, of course. So, for instance, a halfling could take a Thief class at 6th level instead of the standard class bumps for a 6th level halfling. (...)
Like this as well, and i don't see why they couldn't be both viable options: it's like in 3E, you could go for Fighter/Thief as well as Fighter/Chain Master.
I would say that:*
when you pick a class, basic or prestige, you can't change it, and you have to complete 5 levels with it.*
after 5th level you can only take levels in a prestige class or in a basic class you don't have levels in. *
you only get "special abilities" from levels 6th to 10th , like the ability to cast spells, lay-on-hands, or the use of MDoA. *
If the new class would have an higher BAB than the old one, you can use the new BB (this is in replacement of the old attack bonus, not in addition to it)*
Same with each saving throw*
If the new class would have a higher HD than the previous, you can roll to see if one of these new HDs replace a smaller one. Example: a 5th level Thief decides to take 6th level in Cleric: He rolls 1d8-1d6. If the result is greater than 0, add that number to total HPs and recount HDs as : 4d6+1d8.
This way there wouldnt be many differences (maybe just HPs!) between Jon who started of as a 5th level thief, and then took 5 levels in Cleric, or Noj who did the opposite.