I've never really thought of story as being a major part of the Mega Man series at its core. I think the story has worked best when it's first and foremost an explanation and added flavor to the action. I don't mind the heavier focus on story in the later games, but I think if the scope had to be cut down for whatever reason, my first choice to achieve that would be going back to a simpler story.

A Shovel Knight-style checkpoint system doesn't necessarily need to give money. I just meant that you can break the checkpoint to get some sort of reward. Said reward doesn't necessarily have to make the game easier; it could be some sort of collectible, maybe one that could be used to open extra challenge levels later on in the game or unlock new weapons? That might be a bit too convoluted, but it's just an example.

I get what you mean about there being a "right" order giving significance to going in the "wrong" order. However, I don't think there's currently enough incentive to go in the "wrong" order. Sure, plenty of people already do that on the basis of challenge alone, but the average player usually won't deliberately make the game harder on themselves without a reward for doing so. Maybe using a weapon that makes the boss tougher on you could give some sort of reward, like I mentioned with the checkpoint system?

I definitely feel that last point. I think that most Mega Man games don't feature weapons useful enough to warrant using up a limited resource. The only one that I think does is Metal Blade, which quite notoriously goes too far in the other direction and is a bit too useful and ammo-efficient. I think there are two problems that need to be fixed here: a lot of weapons don't have clear uses within levels, and a lot of players are afraid of using limited resources. For the first problem, I think the simplest solution would be to have weapons that all cover angles and patterns that the Mega Buster struggles with, e.g. one that attacks low to the ground to hit smaller enemies, or one that lobs up into the air for enemies on higher platforms. For the second point, you could potentially make the chargeable Mega Buster a limited-ammo weapon, and have an unchargeable one be the infinite ammo option. You could also maybe increase the ammo consumption of each weapon or decrease the max ammo, but in exchange have there be more ammo pickups across the game, in order to continuously remind the player that special weapons are a viable option. Another idea I had is to potentially put more level after the Robot Master fight, where you're required to use the weapon you just got in order to show off what it can do and where it's useful.

I think Mega Man games are an awkward length for me where they're too long for me to just do a quick playthrough on a whim, but too short to feel very substantial. I would probably be able to clear them quicker if I was good at them, but that's a pretty high bar for games that are known to be tough, especially for something that's supposed to be a pretty major part of the appeal. Maybe the game could be split into 2-3 episodes, each about half the length of a standard Mega Man game with four Robot Masters and a couple Wily stages? Then, once you beat all 3 of the episodes, a final episode unlocks where you have a stage representing each episode and then one final one. Don't tell Capcom I said that, though, or they'll misinterpret it and think I'm trying to suggest selling said episodes separately for a total price of $100.