It's fine in MM6 and I think MM4. MM5 is where they really fucked up the balancing. The X games also made the buster too strong.
MM6 mega buster is strong but not stronger than the One-Punch Man charged punch, Jet Mega's mobility, Knight Man's mace or Flame Man's special weapon. MM5 having only shit weapons just leaves you no alternative but to hold charge the entire fucking game.
MM9 removed both the charge and the slide, which was a nerf too far imo. MM10 Proto Man has the charge and slide but is limited to only 2 lemons onscreen at a time and his charge shot isn't that strong. MM V game boy removed the charge buster and replaced it with a charged rocket punch that doesn't travel fullscreen (but lemons do.)
My point is that the charged shot can be balanced well if the developers are thinking about it.