I honestly don't think being an assist trophy really had much of an impact on Spring Man's exclusion. With Spring Man being in the initial line-up, getting used for a fake-out in the Min Min trailer, and Sakurai not mentioning Spring Man's assist trophy when discussing him in the Min Min direct, it seemed like he was just as eligible as anyone else.
Min Min's inclusion looks to be exactly what Sakurai says it was, a request from Yabuki. It's not a conspiracy against Spring Man or an embrace of Min Min as the new mascot over Spring Man, it's just putting a creator's favourite as a character in a crossover fighting game. There's no hard rule that the mascot has to be the first to get into a crossover, as is shown by Zero in MvC3, Mai in DoA6, and Akuma in Tekken 7. Sometimes a cigar is just a cigar.
I do think Sakurai may've started off by considering Spring Man, which would explain why he had the "Spring Man's not the protagonist, everyone's the protagonist!" conversation with Yabuki. He may've brought Spring Man to Yabuki precisely because he believed Spring Man was the protagonist and thusly a natural fit to represent ARMS, which would led Yabuki to say "well technically everyone is the protagonist, so maybe you should go with a fan favourite?". From there, Sakurai would naturally focus in on Ninjara and Min Min, with Yabuki giving his personal blessing to Min Min.
Granted, this is all just conjecture based on a few statements we don't know the full context of, so I could easily be wrong. I imagine Sakurai's upcoming Famitsu column(s) will provide a more detailed account of how exactly selecting Min Min went.