I will open by making the claim that any RPG developer worth their salt is inspired by Final Fantasy. It's pretty much a requirement.
Secondly, it is not made in Japan, so it is not a Japanese RPG (JRPG).
Thirdly, you're making the same mistake many people make when it comes to JRPGS themselves; characters trying to cope with emotional baggage based on a difficult past does not make them JRPG cliches, it makes them good characters. And even then, just because characters are similar to other characters from JRPGs does not make it a JRPG; that's like saying Star Wars is a book because of its ties to Greek mythology and The Odyssey.
Fourthly, "there is fanfiction and the players care about the characters" has absolutely no bearing on genre. None whatsoever. There is fanfiction for everything. You should see the gigantic amount of fanfiction for My Little Pony: Friendship is Magic, some of it is even incredible. Check out the amount of fanfiction for Star Wars, or Halo, or Buffy the Vampire Slayer, all American things across mediums. If people like it, it will have fanfiction, and there is no more meaning to garner from that.
Fifthly, the gameplay of Mass Effect 2 is exactly the opposite of how a JRPG typically works. JRPGs are about a linear story with little to no player input when it comes to the protagonist's personality and strategic turn-based combat that is more about the stats and strategy than the actual act of battle itself (speed, accuracy, etc. are handled by the system, the player simply strategizes and commands). These are both good things; absolutely nothing wrong with them. But Mass Effect 2 dropped most of the stat-based RPG elements in favor of a more action-centric battle system and has huge amounts of player control of the protagonist's choices and personality.
This discussion was over as of that second point, but I figured I'd point out the other issues. I'm sorry, but this argument simply doesn't hold up.