Multiclassing in Pathfinder RPG does not allow the mixing and matching of alternate classes with the classes they are based on. I am left wondering, why is this the case? I can see the logic with respect to the Paladin/Antipaladin, but see no good reason why rogues and ninjas and perhaps the cavaliers and the samurai should not be allowed to multiclass into their respective alternate classes.
For example, a party of characters sets of on a journey from the Western cultural area to an Eastern cultural area, where they eventually become acclimatized. The party wizard, sorcerer, fighter, cleric and even paladin can benefit from the specialized ninja training offered, but the rogue, who should find it the easiest to learn, cannot. Ugh.
By contrast, I see nothing suggesting that Archetypes cannot be combined, provided that they are cued of of different abilities. So why the arbitrary restrictions against Alternate classes? Come to think of it, what's the point of having alternate classes at all? One could just as easily have them as base classes without any harm being done other than base class bloat. Such bloat might be undesirable, but alternate classes don't exactly help in stemming the tide, as they pretty much add to the same bloat just under different name. Failing that, these alternate classes could simply be turned into archetypes.
Combining archetypes can be done without messing up the normal class progression they are not multi-class but you swap out several abilities, and then swap out some more.
Alternate classes are the same class and do not build upon each others progresion, they are too different to fit into an archetype but too similar to multi-class, allowing odd-ball combinations. I think there is little benefit to be had allowing it only being good for metagaming combinations/level dipping. If you can make it work with some houseruling simply allow it, but you will run into similar abilities that oddly do not stack, are too powerful if they do or make for some complicated and unneeded rules.
Troll?
To answer your question. The Archetypes cannot be stacked because even with replacements some still give the same ability. What happens if I multi-class synthesist summoner with normal one. Can I have both my suit and my external familiar? Do my levels stack? If I can have both, what happens when I choose to only have one; can I use the spell like summons tied the the currently non-summoned creature? Questions like this will pop up all over the place.
Now as far as your dislike of archetypes. The archetypes in ultimate combat were numerous yet they only took up 54 pages. If each of these had been fleshed out in full class format they would have spanned a much greater length. This is impractical from a cost, as well as layout standpoint. One more problem with expanding archetypes into classes would be the mass number of redundant abilites. The current archetypes, if classes out, would have to spell out all of the new abilities as well as all of the original class abilities. As it is now only the new stuff is written down.
Hopefully this was helpfull and not just morning wake/bake ramblings. If you really want lots of classes, just use your 3.5 books. Pathfinder was designed so that you could do that...
to respond to the comments in the OP, a rogue can receive ninja training and do it easier than any other class. He does it by just taking Ninja talents in his rogue talent slots, so he is a ninja w/o multi-classing but everyone else has to dump one of their class levels.
a Cavalier can switch his oath to one of the samurai oaths.