Gestalts are by their very definition "Multiclassed". The method is basically identical to what a character in 2nd edition Advanced Dungeons & Dragons would do to become a multiclassed character. You're taking two classes and effectively gaining levels in both classes at the same time. When I read Unearthed Arcana, my impression was that the DM shouldn't allow players to take more than two classes and do this, nor were the classes meant to come from the same category (For instance, Fighter/Wizard is ok, but Sorcerer/Wizard is a clear conflict of interest in Gestalt. The point of the Gestalt option was to give a weaker class like Wizard or sorcerer better hit dice and save options).
Actually, Sorcerer/Wizard was one of the listed "particularly potent" combinations of classes in Unearthed Arcana. There is nothing explicit in UA that says that you have to keep the same classes throughout all twenty levels, in fact, it does have rules regarding prestige classes. (only one prestige class at a time and no gestalt PrC's)
This is a gray area between RaW and RaI.
The closest thing to PrC's in 2e were Kits which were chosen at first level, and if I recall correctly, your multi-class was chosen at level 1 and locked in. it just was beyond complication for the Fighter/Thief Elf to dip into the arcane and suddenly become a Fighter/Mage/Thief.
Third Edition opened the multiple class doors wide open, by allowing you to play a charcter that was lvl 1 in every class, your character would be an inefficient and underpowered build, but it was possible.
I am contemplating running a Pathfinder Campaign w/Gestalt, and While I would rule of people being locked into the two classes, Rules as Written just say "Each time he gains a new level, he chooses two classes, takes the best aspects of each, and applies them to his characteristics."
The caveats listed after that pertain to class features advancing at the faster rate(not stacked), spell lists/spells per day are kept separate, the aforementioned Prestige Class restrictions, and no variant classes with base classes.
However, to address the concern that has been shown about taking a second class... make the Gestalt class non-unique, which lets the user add it more than once. As it is, you have to add class levels of base classes more than once anyway. Each time a level in Gestalt gets added, the user would choose which classes are gestalted together. I still think it could be done with just one class instead of doing every single possible permutation out there.
Actually, something similar to this is what ShadowChemosh did with his beta released Mod. It is still in beta right now, but works in a similar matter.