You can put as many games as you want on the microSD card.
The 3-in-1 uses two different kinds of storage, though... one that's temporary (and holds up to 16MB) and one that's flashed (and holds up to 32MB). If the GBA rom you choose is 16MB or less, it will load up right away and be stored in the temp memory. If you have a rom BIGGER than 16mb bu less than 32mb, it will have to be written to the flash memory (which will take a little while).
Other than that, there's not much difference as far as I can tell.