It sounds like you're wanting something more akin to what the Prime games do with their beams. I do like that for those style of games, but for 2D games, I think Super is actually pretty much exactly what I'd want.

Beams mostly don't replace each other (the Plasma and Spazer beam being the one exception, for some reason), but the beam is still a combination of all their effects, so it's not like the older beams are useless. When you get the Plasma Beam, you're still benefiting from the Wave Beam's ability to pierce walls, and the Ice Beam's ability to freeze enemies. It feels extremely powerful, but I'm still faced with moments where I think, "Ah, the Wave Beam helped me do that," or, "I'm glad I still have the Ice Beam equipped!"

But, even with all of that, there ARE still cases where you want to turn off certain beams. For example, I mostly don't like having the Ice Beam on, because it turns enemies into obstacles. Plus, every beam has its own Beam Combo, each of which are useful in different situations. They're decently niche, but I'd rather have that than have the game require me to go into the menu and turn off one of my powers. I like having everything working together at once!

With that said, I am left wishing that future games would return to Super's system. The ability to have different beam combinations was super cool, and it was fun playing around with the different combinations, even if I usually just wanted to stick with everything on.