Proto Man Mode was okay. I agree, the charge is hardly useful, only at very specific moments. 99% of the time it is better to spam your regular buster.
I still have to play with Endless Attack a little more in order for me to rate it. From what I have seen, it's been pretty nice.
Hero Mode was alright, but I have high expectations for Superhero mode, especially after reading your post. The mode cannot be as cruel as Mr.Perfect, because that challenge is truly difficult for me to achieve. Speaking of that challenge, now that I think about it, it really is not a "fair" challenge, it's actually the hardest task in the whole game! I always considered myself a good Mega Man gamer, but I never thought of this particular challenge when playing other Mega Man games. Just think of cruel games such as X6, and then try Mr.Perfect on them. Oh My God. Good thing to know that it is entirely optional though.
And as for Special Stage, I have only played it once, but other than the decent music, I will not play this stage that much I think. Fake Man was a surprise the 1st time, but now he is awkward to fight.
Remember though that the DLC are just bonuses with a charge.