Am I the only one who thinks it could be/wants it to be the fact that you can ride on certain Pokémon? The idea was implemented in Ranger, and with the introduction of Walking Pokémon, the larger Pokémon's sprites are already there, they just need to be tinkered with...
It's true that the larger sprites would be easier to adapt, but a slightly-enlarged version of a sprite combined with some form of the bike-riding player sprite could easier produce a suitable Pokémon riding sprite, no? And of course, as with any learnable move (should a move be used to access such a technique) only certain Pokémon would be able to learn it, thus GameFreak can pick and choose which Pokémon are ridable as suitable forms of transport; I would say anything large enough and quadrepedal would fit the requirements, as would larger Pokémon such as Doduo or Dodrio, thinking along the lines of the Capture Contest sections of Pokémon Ranger and with Yellow from PokéSpe in mind. I would also class all third-stage Starter evolutions in there, just because they would probably be large enough and the emotional attachment would probably make players favour these Pokémon as their preferred mode of transport.
On the subject of an item, such as a saddle, granting this function accessible, size would again be the main requirement. Only Pokémon that the saddle would fit upon (i.e. not too small) would be able to wear the saddle and thus be rideable. There is also the consideration of Pokémon that are especially large, but the game physics would most likely gloss over the fact that there are no saddle straps in the world that could extend around the belly of a Wailord but still tighten around a Ponyta, so this is not as large an issue. It is just the thought of a Totodile wearing a saddle that is bigger than it that makes me stress the fact that size would be a consideration - I still resent the fact that a Pidgey can carry a person across a region without difficulty, or that a Goldeen can ferry someone across an ocean without a hitch, but as I said, game physics certainly aren't always the most logical and as such, the programmers probably would not see a problem.
