This is a fantastic game. You and your team should be proud of what you have made. The improvements compared to the original Wily Wars, the additions made to MM4, the things equally *maintained* in MM4, the gameplay modifiers, the QoL options, the references/easter eggs... there is just a lot of upside to this. This has the potential to be one of the best fan games of all time, so I'm looking forward to seeing how MM5, MM6, and whatever modes you add (assuming at least a Wily Tower variant) will go in the future.
That said, there is a particular bug that I and a few others that I talked to that played the game have found. There are times in which after defeating a boss, the game no longer continues; can't move, pause, etc. The game basically softlocks. What I've noticed that it may be connected to the type of boss explosion used. The new boss explosions seem to have no issues at all, and the softlocking occurs when the old explosions are used. For example, the Dive Man re-fight seems to suffer from this after beating him in his boss rush teleporter. You can't move or escape from the room to continue on with the boss rush. The same happens during normal Bright Man fight assuming you're not using the weakness (it continues on otherwise, somehow). I don't know what other cases suffer this, but these are the two outstanding examples so far. Hopefully, this will be looked into (beyond the aforementioned two cases) and updated because this game has too much positive value to have this lead to an unintentional negative experience.
It should be noted that I was using Bizhawk when checking into this. If anyone has a similar experience with real hardware, it should be noted as well so all bases are covered.
Looking forward to future updates and improvements. Well done and good luck.