There should be multiclassing but limited so that you have your main class but are able to add in a limited amount of pieces of other classes. Also you shouldn't be able to select specific traits of the others but only predifined sets of their feats and some sets are prerequisites of others, also not the whole set is chosen at once but everything in a set becomes available to chose from on later level ups.
For example let's say the fighter has a set of basic melee feats and a set of swordfighting feats and you as a mage want one or more of those swordfighting feats then first you would have to gain access to the basic melee and take a certain amount of feats, perhaps even some specific ones to unlock the ability to make the swordfighting feat-set part of your levelup choices. Also the amount of sets out of classes foreign to your chosen class should be limited.
Prestige classes should be handled the same, each prestige class gets one or more sets of feats, again with dependencies within and between sets and a limited amount of possible sets active at the same time. So let's say the amount of prestige sets is limited to 2 then you could either take the low tier sets of two PCs or specialize in one by making your second choice a high tier set of the same PC you choose first.
Also both, multiclassing and prestige classes, should have prerequisites within the main class, for example a cleric could a have a set of melee feats, which, if he puts enough choices into, would allow him to make a set of the warriors weapon specialization sets part of his multiclass choices. So your non-warrior has to go somewhat into the warrior direction before he can multiclass into it.
Now there is the problem of what to gain if i don't multiclass. My solution would be to add end tier sets to each class, which can only be taken if you mained into that class and take up several of your multiclass choices, for example the magic school of "utther destruction and world domination" could only be taken by someone who mained in mage and hasn't taken any multiclass choices while the school of "quite some destruction and nation subjugation" could be taken with 3 free multiclass choices but again only by a mage (only problem now is to make those high level abilities worthwhile without making multiclassing worthless). This way could even be employed for prestige classes, you have for example 6 multiclass choices and each prestige class set needs 3 of them. This would depend on, if prestige classing is something that is seen as a fixed part of progression or an option.
