I have always had controversial feelings about 3ed multiclassing and Xp penalties.
On one side, multiclassing in 3ed works immensely better than any previous edition, and leaves any possibility open (for example, no race restrictions) to any character concept, provided that the player takes some disadvantage when he goes too far. This is good, because IMHO if a player has a concept he wants to develop about his character, there should always be the possibility to do it, if it makes sense obviously.
On the other side, 3ed multiclassing quickly became exploited by every so-called powergamer in search of the best combination to maximize his character, and concept usually follows the maxing choice instead of vice-versa. 3.5 attempted to spread class abilities over more levels exactly to lessen this kind of abuse, but obviously it won't get rid of the problem totally.
Furthermore, I still like D&D as a class-based game rather than an ability-based game; I know that's my view anyway, and others hope it to become less class-oriented. Usually, multiclassing or "prestigeclassing" is said to be a mean to versatility, but 90% of the time is used as a mean to specialization, i.e. exactly the opposite.
Back to the Xp penalty, it's probably difficult if not impossible to come up with a rule which would 1) allow any combination without spoiling good RP ideas, and 2) avoid exploiting powergaming. A rules lawyer or munchkin (very often the same person aka "ruleslayer"
) will always find the hole that lets him make a pesky PC without penalties.
It seems to me that the original idea beyond the Xp penalty was to freely allow these kinds of characters:
- single-classed
- multiclass evenly in 2 or more classes
- basically single-class but with few levels in another (provided that one of the 2 is the favored class)
PrCl don't give Xp penalties IMHO because you always get the 1st level when you are at least a 6th level PC; if you got Xp penalties, you had to be of your favored class to get any PrCl.
Ultimately, the DM is the only one who can encourage sensible multiclassing. I would allow anything by the rules, but if one of my players had more than 2 core classes and/or more than 1 PrCl, it's definitely going to be difficult for him to RP his PC: as I used to give RP award (in Xp), even if he doesn't have an Xp penalty by the rules, he'd better have a very good reason for such a PC, play it excellently, or get few RP Xp from me.
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A side note:
I don't think the Archmage and the Hierophant are a PrCl the same way the others are. A PrCl is normally some kind of specialization, possibly associated with a group who holds specific knowledge otherwise unavailable, which usually takes a PC through its levels with little interruption (unless you took the PrCl for munchkininsm).
Acm and Hie don't show any progression deeper into a field; every single level of those classes gives the same as the other levels (don't look at BAB and ST for this purpose), which typically is a single and very special ability freely chosen among a list. They work exactly like you were spending a level worth of Xp to buy yourself a specific ability by choice. For this reason I really like these 2 PrCl -- note that normally I HATE PrCl with less than 10 levels! -- and unlike the other PrCl I think it makes sense for a PC to get just 1 or 2 levels, and maybe every 10 years or so.