Everyone here has been overthinking this problem.
The whole point of 3rd ed is that it is
character based, not
class based. To this end, the bonuses of the classes
stack with each other. So if, for example, I take 8 levels of fighter, I will have a tough as nails character that is totally focused on fighting- high HP, great att bonus, extra attacks, etc. However, if I take 4 levels each fighter and thief, then those levels bonuses add up and stack with each other- I won't be as strong as a straight fighter, but instead I will have a bigger bag of tricks- more skill points, the ability to flank/backstab, etc. The end result in both cases is that I have 8 full levels of power (for lack of a better word) that I have distributed as I saw fit.
This obviously applies to all classes, even spellcasting classes- a cleric who takes a few levels of mage may do so just to have access to arcane abilities. That character won't be as "clerically" powerful as a one that is a straight cleric, but instead will have other abilites that the straight cleric doesn't.
If you are confused about why it takes so much more xp for a 16th level cleric to gain 1 level of mage than it does for a 0 level character, think of it this way- the high level character is gaining his/her 17th level
as an individual, not the 1st level as a mage.
This is the primary difference between 2nd and 3rd editions. In 2nd ed you were locked into your class, and if you could dual class, you had to stop using your old abilities until you had caught up in your new class. 3rd ed is kind of like a smorgasbord for character levels- a few here, a few there, and the end result is a much more unique character.
Ironically, because 3rd ed allows much greater levels of multiclassing, people usually end up focusing on one class to a greater degree because the further along you get in levels, the greater payoff each level is in that class.
Edit: I wrote a little about this regarding kits in the
D&D online forum