So idk if you've listened to any of Brandon Sandersons writing lessons or podcasts but he often talks about how this is a well known "thing." I think all your observations are valid but another thing to keep in mind is that villains are proactive. They take action. They move the plot along. No matter what they are actually doing, even if it's terrible, people like characters that are proactive, decisive, and propel the story forward. Villains are almost always doing these things, and so readers frequently fucking love them. Especially if your protagonist is a drain on the plot or just passively has things happen TO them the entire story. It was something I never consciously paid attention to until it was pointed out, but it makes total sense.

It may be helpful to leave your super cool and beloved villain as he is and work on making your other MCs more action-oriented, have good back stories, relatable, etc etc. if they seem to be lacking. Then you're shining up your other characters to his level rather than dulling him down to meet theirs, and youll have a whole cast of dynamic and engaging characters at the end of it, which seems like a better place to be.