So, the other day, I decided to reset Dr. Light's missions, due to training Proto, my fire robots and the new abilities. The problem is that the button isn't 100% working, as my mission progress WAS reset, but the missions didn't generate again, leading to the exact same battles. Basically, it resets missions, but doesn't regenerate them (Fusion Fields and Wily Stage IV). Also, the fusion fields started in Hard Mode (Robot Masters instead of Mets), thus making the button almost useless. I double checked today, and neither did anything change.
[b]LOCKED by Adrian Marceau as Fixed on 2013/10/23[/b] If this bug resurfaces please create a new thread. Thank you!
The "Reset Missions" button is not working correctly Posted by Shadownnico on July 12th, 2013 at 10:57am Viewed 318 Times
Chapter 3 Oil Mines Clock Warehouse Steel Tower Arctic City
As you can see the first 8 missions will always be the same, but they'll be presented in a different order. This is what affects the combinations in Chapter 3 (it works the same way for the later chapters). I guess it's possible that your randomly generated missions ended up in the exact same configuration, but it's incredibly rare and unusual that it would happen and I wasn't able to replicate it in my run-through.
Regarding the Wily Stage IV, that counts as an "event" mission and will therefore always be the same. At some point the collection of standard RMs will be replaced with "bosses" (Yellow Devil, etc.) but for now this part is static and unchanging no matter how many resets, sorry. :S
Lastly, the Hard Mode bonus (which is exactly what I've been calling it) is unlocked after you've made it to and completed the Bonus Field battle and the event-flag cannot be removed through the "Mission Reset" feature. I can see you've done this with both of your characters as they have little icons next to their name on the player select and the save menus (a heart for Dr. Light and a clubs for Dr. Wily), and that's why you've been seeing RMs instead of Mets on all the fusion fields.
I hope that makes it a little easier to understand how it works, and I'm sorry I wasn't able to replicate the other bug you mentioned. Let me know if you think is this a bad bonus or if you think it should work a different way, and I'll be happy to reconsider. Thank you for your feedback! :D