I disagree, I think there is drama in Mega Man being unable to stop Wily from taking one of his siblings for evil intent once again (which would add further reason to his outburst at the end of the game).
From an explicit game perspective, the point of including that scene is to raise questions as to what Wily is planning with the GutsMan. If it was all just about the siblings appearing again and doing evil, then they would have just appeared at random without such an introduction, after all, it's overdone and is not special within the series. See World and R8.
In this case, they added this scene to make you feel and think about what's coming sooner or later; the built up to the battle with GutsMan modified to GutsMan G. There is no definite need for it to be the original. As the original, the drama of "why is GutsMan deactivated?!" conflicts with the drama of "Wily is taking my brother!". A scene in which the original GutsMan is brought to his knees after failing to stop Wily is far more dramatic toward that end.
Besides, two PlantMans.
I question the logic in saving time and effort by going out of your way to steal a museum replica, since it could've been made of clay for all we know. The only reason it could be worth for Wily to even bother breaking into the museum to take the robot would be if it was either the original or a functional copy (and it would be a total waste to built one just to put it up for display).
As has been proven by World4, the museum robots are all functional. Just being on display does not mean they'll never move. Besides, your own logic applies to the original, why would they have a functional original there? It's far more of a waste to remove the original GutsMan from his job than it is to built a display copy.
this is inconsistent with their Guts Man page where they state Guts Dozer and Guts Man G as rebuilt versions of Guts Man.
When it comes down to it, the minor enemy pages are more consistent than the boss pages. Given the way AF's encyclopedia was integrated into MMN.
Either way, GutsMan was alive and well when Wily built the Guts Dozer/Tank. (R1/RR to R2) The meaning of "rebuilt" here is not "repair", it is "building again from the same plans." There's no mention of it being the same mind and are explicitly said to be other forms. Guts Tank entry also explicitly says it is just modeled after Guts Man.
The statement of Guts Man resenting Guts Man G could be interpreted as an experience which he regrets, so...
They're referred to as "creations" not "his own body getting mangled."