Solrock and Lunatone are meteorites from space. Plus everyone else mentioned Cleffa, Starmie, and the Isshu aliens, so they probably are. How they came into exsistence is a whole other question. It would probably be a PokeDarwinism vs. PokeCreationism debate, and that would get very loud
Then again, Pokedex entries should be taken with a grain of salt (remember, Magcargo is hotter than the Sun!). Plus, how is it that these other-worldly beings could be classified as Pokemon and mate with Earth creatures? Having alien Pokemon seems to bring up a lot of questions the more you think about.
No idea about alien trainers, though. Just because there are alien Pokemon doesn't mean there are also alien humans. The alien Pokemon might actually be the rulers of their planet! The non-Pokemon aliens could be treated like Earth Pokemon!
Lots of questions and lots of possibilties, that's all I know on the subject.