What don't you like about it? In Super metroid the controls felt weird for sure with space jumps but I never thought they broke the design badly, and on the contrary I thought Metroid Fusion had good level design that made space jump feel empowering without completely bypassing all challenge or generally feel like breaking anything.
I just don't like.. flying. I don't think it controls badly, I just think it is *too strong*. Walljumps are fun, things like Grapple Beam or Hookshots are fun, Doublejumping is fun, etc.
Flying just kind of takes out all platforming and "removes" large parts of every room.
See: Super Mario World staying at the top of every stage avoiding everything forever with Cape
Now, certainly it is possible to build things in a way that the flying is somewhat interesting and doesn't just kill every room, eg Fusion does this well in the Secret Metroid lab where you have to climb vertically quite a bit but get interrupted a lot by erratic Metroid movement. But if you do that, then I think SpaceJump is too.. silly. May as well just make it "Hold Jump Button activates Jetpack" or something to that effect.
SpaceJump just has no downside and no limiters. You can, and will, use it everywhere and just lalaland through everything after you have it (unless the Rooms are intentionally designed to stop you from doing that by eg all being horizontal rooms with a low ceiling or vertical ones with tons of obstacles, but then what is SpaceJump even there for). Shinespark needs room to get charge, figuring out where to use it, and then it costs life (well, at least in SM - which I think was a very good decision). Grapple Beam can only be used in specific locations and is a bit clumsy. (SingleWall-)Walljumps take a bit of practice and again can only be used in certain locations, Infinite Bombjump takes forever and has limited applications, etc.
SpaceJump is an "always goes" magic button. At least give it a timer and a cooldown ("You have 'infinite' jumps, but only as many as you manage in 5 seconds - after that you have to land and wait a bit for it to recharge"), or make it cost Ammo ("Samus propels herself forward in midair by shooting a missile") or what have you.
But i mean, both in Super Metroid and in Zero mission, all alternative paths and routes and sequence breaks were intentional, or at least the devs knew it was possible to work around. =P
"DeerForce intended it" is a running gag in the SM community, but I kind of doubt they knew about Mockball, CWJ, the entire RBO route (from Hellruns to suitless Maridia), any of the large glitches (triggering the escape sequence via XRay climb.. heh), or even "simple" things such as horizontal Shinespark over the Moat towards Wrecked Ship (or even SingleWall-Walljumps! Which I don't know whether they were intended).
http://www.twitch.tv/zoasty/c/5768579?t=9m11s If you think the Devs "knew it was possible to work around" the game like this.. well.. I would disagree :F