Megaman and Castlevania are not Nintendo IP's, that is true, but most of their popularity is based on the early games on the NES. People have more fond memories of Megaman 2, 3 or X and less of later games like Megaman ZX(A) (still Nintendo, I know) or the blasphemous excuse of a Megaman in Street Fighter X Tekken. Same goes of Castlevania, people like Castlevania 1-4 more that Lords of Shadow.
Going back on topic, I have a 2 part Megaman X RPG based on the Starwars d20 rules. It's already quite old and made in Word files, so it might be a bit buggy. Here is a link of it.
Im playing a character with a Samus Aran based class right now in a homebrew centered campaign. If he dies, I have a character with a Link based Class ready. Maybe you already found these? I also have a friend who played a Pokemon Trainer class, but i don't have a link for that one. We changed the name to 'Jewel Summoner' who uses crytals instead of hi-tech metal balls, but it was basically the same. Mostly to get rid of the Pokemon name, but also a little bit to fit the setting.
Try to put a bit of focus on one specific setting and build all the others around it. Bows might look nice next to laser guns, but it makes hardly any sense (unless of course.... aliens... I guess... or Smash Bros).