We chat about videogames and videogame accessories.

What do you mean by "freedom of movement"? The other two points apply to Mega Man Zero 2 and that's clearly stage-based, so this would have to be the deciding factor.

As for missions, I don't think the idea of missions is inherently in conflict with the idea of a platform adventure. Rather, I think the type of missions presented in MMZ are in conflict, because they're designed as stages (backtracking is possible, but not encouraged in any way and literally every design choice is about pushing you to keep moving forward) and have the presentation of stages - you pick one from a list, you get transported there, clear the stage, get a ranking screen and are brought back to base. If not for the physical connection of how you revisit them, they would be unambiguously stages, and this is easily shown by looking at MMZ 2-4 where this is the case.

I'm asking this because I really don't understand the difference between where you're drawing the line and where I am in this case. My position is, essentially, the elements that keep MMZ from obviously being a stage-based game are superficial and completely incidental to the game design. Do you think that they aren't, in which case could you be clearer about why, or do you agree that they're superficial but think they still count towards classifying it even so?