I'd prefer not multi-classing by itself, but having possibility to go on with Prestige Classes (in the specialization tree manner) after certain levels, e.g.:
1. you choose your main class in the beginning
2. you choose 1st prestige class starting 4th level (this class is obtained from the list, correspondin to your main class - let's say 3 options)
3. you choose 2nd prestige class starting 10th level (this class is obtained from the list, corresponding to your 1st prestige class, let's say 3 options for each)
4. you choose 3rd specialization class starting 18th level (this class is obtained from the list, correspondin to your 2nd prestige class, let's say another 3 options)
5. etc.....
The idea would be, that there are prestige classes, which have according pre-requisites and it is the only way to multi-class (i.e after you choose mage, you won't become mage/fighter, but you could decide to become battlemage, instead of being pure mage)