It's probably because it's a more complicated subject. Not everyone knows about polycount, CPU cycles, extra face/body models, or even basic programming. Also, since it only applies to the few characters using the most resources the first thought that comes to mind is to remove or hamper them rather than make them more efficient. Ice Climbers, Olimar, and perhaps but probably not Pokemon Trainer, are the only real issues due to multiple characters.
Oh, and Brawl modders can shed some light: each alternate costume is a different file altogether. 4 Olimars have the same model, but is loaded in memory 4 times (Pikmin included) with different textures. Reducing that inefficiency to reuse the same model whenever possible would reduce the memory usage to a quarter of the space. Cases like Wario and Pikachu may use a different model for all 4 characters anyways, but for the actual cases where memory would be a problem (Olimar, Ice Climbers, Pokemon Trainer) there are no separate models. But I'm no 3DS programmer, these are just educated guesses.
That may be true. I could certainly imagine Pikmin behaving in a more static, simple way to save on CPU speed.