Immoli: I only played the GBA ones, but it seemed like most of the upgrades were equipment with stuff like +10 attack or whatever.
I like how Metroid gave abilities that added utility and whatnot.
Plus Fusion and Zero Mission would place markers on your map suggesting where to go, even if not saying outright where to go as opposed to having to search around finding that one place that you passed up before and can now progress in. And movement felt faster in those games.
That was actually something that I disliked about Fusion & Zero Mission. Super Metroid had such good level design that you "knew" where to go next, without the game having to outright say where to go.
Good level design can do that, it will point you in the right direction, while making the player feel like (s)he is exploring and coming to conclusions on his/her own.
Also, the Metroidvania castlevanias had more than just "+10 attack", they gave you new abilities as you went along, thus allowing you to access new areas. This is what the Metroid games did as well.