Another way to control multi-classing, a little like the Spycraft method is to make one basic ability unavailable if you class into it later.
This is off the top of my head, so be gentle...
BBN: No Fast Movement
BRD: No Bardic Knowledge
CLR: Only one Domain
DRD: No Nature Sense (and obviously No Animal Companion)
FTR: Could be free-access otherwise no initial Bonus Feat
MNK: No Evasion
PAL: No Divine Grace
RGR: No Ambi/TWF proficiency
ROG: Could be free-access otherwise no Trap-detection
SOR: No Familiar (must quest for one)
WIZ: No Familiar (must quest for one)
You could maybe allow purchase of the ability by expending XP.