There's Dragon Quest Monsters: Joker. It's a shame they went for the fusion route, I've never liked the idea of wiping out two monsters I've worked on.
The guy that made the MARDEK RPG games made a couple of half finished pokemon clones you can find here http://www.fighunter.com/?page=games
Insomniac used to have a browser game called Outernauts where you could catch monsters in space, breed them, and fuse them. Last I heard they shut it down due to not gathering enough whales.
If you want to combine your monster trainer itch and smut eramegaten is a pretty good game in itself even when ignoring the smut.