I was just a bit too old to get caught up in Pokemon fever. They seemed like fun enough games but I think a big part of their draw these days is nostalgia. Being that I'm a big nerd I feel like I'm missing out to an extent, that it's too late to jump in. I'll never have that attachment to my first starter Pokemon, or be able to remember 100s of little monster's names.
To my knowledge Deoxys is the only alien Pokemon. It arrived as a virus on a meteorite and continued to change into this form. I'm fairly sure it's a powerful antagonist of some sort.