I haven't seen everything you've referenced, largely because I'm not a weeaboo, but I'm not seeing how unintentional similarities is a point against the show. It's a sci-fi comedy, of course it's gonna play with well-known sci-fi tropes. That's its whole thing. For example, what's the rip-off of The Matrix? The federation prison where people get strapped in small containers and interrogated in simulated worlds? Yeah, people have done that gimmick since well before The Matrix. It's kinda hard to do an episodic sci-fi show and not include some kind of simulated world. Or, at least, it's not surprising when something like that shows up.
Mr. Meeseeks is clearly a reference to
House of Cosbys, another show made by Roiland on Harmon's old channel. Yes, the Cosbys aren't disposable, but they're annoying and eccentric disposable clones that are made to help out around the house but quickly spiral out of control. Again, there aren't any completely original concepts out there.
Your problem is assuming that Evil Morty was intended to be a big thing. I remember there was
a con panel where the fans asked about Evil Morty for Season 2, and Roiland and Harmon didn't have anything planned. Evil Morty was a one-off character used for a big dramatic finish of one episode, and the fans kept demanding he come back. Then they decide a giant fanservice twist next season, and hey the fans suddenly assume Evil Morty is going to be the season's villain. When it turns out the season is just going to finish on a normal episode, like, you know, episodic TV shows normally do, suddenly it's Harmon being too edgy to include the finish fans psyched themselves up for.
Harmon has a lot of obvious flaws, let's not make up bullshit for why he's a lolcow.