Ah bugger it! I made this giant post for Samurott and the page failed on me!!
Here's the gist of it anyway, switching eras and characters (just to help out, and the recommendations i would make, i know ff roles may be foreign to you);
Present; Now, I know you said you wanted Riolu to be a Future character, but this makes more sense to me. Riolu, either http://finalfantasy.wikia.com/wiki/Monk
, or if you ask Oshawott nicely if you can have the same job, as aura works the exact same as Chakra, consider these if you watch or read Naruto; http://naruto.wikia.com/wiki/Ninjutsu http://naruto.wikia.com/wiki/Taijutsu
Middle Ages: Dragoon Charmander is dead-set perfect for this era! Because it's mythical, and I compare him standing next to Knights in that era. Charmander in Dragoon armour would look awesome. Plus make sure to have the weapon as lance/spear and have the Jump Skill, a Dragoon's famous ability.
Future: Dewott... In the last post that died, I wrote that if Riolu didn't get a job pick, you'd put that job onto him. I like that you're thinking about future character job roles, but right now present characters are the most important. Otherwise if you pick Ninja for Riolu, Dewott could be a Blackbelt/Monk. I'm uncertain of my future characters as well, which is why I only said to reserve two pokemon, not pick roles immediately.
Glad to have you aboard, Dark! Regarding your questions; pokemon will not evolve in this roleplay. However, if that have an Ultimate Attack, that say, takes the golden or spiritual form of the evolved form of that pokemon, that's more than okay. Evolution is more or less based on age really, although not actually seen, my Wartortle, for instance, may have had a Blastoise dad. Obviously we see this as the father being older, etc.
For the family idea and the gens being in particular eras, it clashes a hell of a lot, doesn't it? So, particular gens will in fact only be used for the monsters (feral pokemon) we fight. Otherwise, environments may still have other species from other gens as well, we'll see. But right now I'm getting ahead of myself lol.
In other words, your family and species is not restricted to gens, just common sense and whether you picture a human-like nature in these pokemon.