That stuff works. No MU* should be expected, and no MU* can ever support, having EVERY PLAYER involved in EVERY PLOT.
We had an entire world grid mapped at various Transformers and Megaman MU*s, and different things worked for different characters. People find out about Ming's invasion via spies. The people on the ground and closest to the launch sites get to go all Rogue One on it; the assassins? Intelligency types get to shine.
Build your plots to cater around, not just 'HERE'S A PLOT EVERYONE HAVE AT IT'. It's unrealistic and, in honesty, at least to me, not fun. If I'm a fighty guy, I'm not going to go be the head of an intelligence gathering or building something plot. If I have no raygun skills, I'm not going to grab a raygun and go to the front lines. You just have to have an understanding that, not all plots are made for all characters. I would HOPE that players on MU*s would think the same thing, but...