Just throwing out anything that might be relevant here... According to Super Mario Advance, Clawgrip was a Sidestepper affected by Wart's magic. If Subcon is an actual place, which is possible, then my theory would be that the Sidesteppers originated there but were hunted to near extinction. Some formed underground colonies, which were also nearly eliminated eventually, and others found their way to Earth. Subcon being real isn't necessary yet, but I'm sure it will at least be helpful someday. I don't have any problems with Shy Guys, but if Wart ever shows up in Mario Kart, we'll have a problem. He was already in Link's Awakening, and it can be argued from Wind Waker featuring Earth's night sky that the Zelda games take place on Earth or a parallel dimension thereof, which would fit.
Fighter Flies in the Beanbean Castle Sewers... Either they're inherently drawn to pipes, or the Beanbean Sewers are somehow connected to the Brooklyn Sewers. I could see there being some sort of interdimensional transport in the BBS, since we know they're probably not used as actual sewers. What do they do for sewers? Wait, do the Beanbean people even need sewers? There's a good chance they're photosynthetic, so they probably don't even produce waste. So if Mario and Luigi had known more about the Beanbean race, they wouldn't have fallen for the trap. There's an interesting aspect. Anyway, I guess Bowser took over the Mushroom Kingdom first, and the Beanbean Kingdom set up Little Fungitown for refugees, and then Bowser took over the Beanbean Kingdom, using the BBS link to try and take over Earth.