Joker is not getting in. Sega getting three reps will be overkill. Also, his entire franchise has never touched a Nintendo console outside of spinoffs.
And Cloud never made a single appearance outside of spin-offs on Nintendo systems. The franchise has made Nintendo appearances.
Your reasons don't actually really do anything to explain why he can't get in. Sega getting 3 reps? Doesn't matter. It's a matter of how easy they are to get, which considering Sega is very friendly with Sakurai overall, makes a Persona/SMT character actually pretty easy to get. The only real competition for Joker is Jack Frost franchise-wise.
We also know that having a Nintendo appearance isn't even a requirement, though it is helpful for sure. But even if Joker never had one, he'd still be fairly easy to get compared to some characters just due to the fact that Sega is far easier to work with than some. There's a reason Bayonetta got a crapload of content compared to Cloud and Ryu. Never mind Sonic as well. Licensing gets easier with companies who are more likely to work with you.
Ultimately, his chances are actually pretty good. Considering he has... one character as competition and all.