She kind of was that way in Spirit Tracks... although she was technically like "dead" sorta....
She wasn't dead, just disembodied (also a total wiseass about this particular matter).
I also kinda still lament the fact that they didn't go through with the idea of having 3 playable characters (ala Secret of Mana) for ALttP. Granted, I can't really lament it too much simply because ALttP was amazing as is, but it would've made this matter less of an unsurmountable issue on precedent (much like Peach's playability status in non-spinoff Mario games).
Isn't having three playable characters on screen the major reason why SoM has a bunch of issues with collision detection/framerate/frite splicker/occasionally dropping attacks?
Given Nintendo's fondness for polish and technical not-being-not-polished it makes sense why they didn't go with 3 playable characters (granted, you could've gone the Rolan's Curse 2 route and just had one playable character active at a given time. Also I'm sure there's another game that did the same thing that people actually played and would work better as an example here but screw it I love RC2 [Noooooot RC1 though. That uh... No]).
There's Castlevania 3 or that awful NES Teenage Mutant Ninja Turtles game if you wanted something less obscure than a pair of GameBOY games.
But no, the reason why SoM had collision detection/framerate/etc issues was in part due to the game originally getting downgraded from the planned Nintendo Playstation design, and in part to the issues with the engine itself (as Secret of Evermore suffers from the same issues despite having fewer playable characters).
And also, SoM was a SuperNES era Square game, all of which were barely held together by Duct Tape, Shoe Strings and Gum.
That said, regardless to the technical feasibility of a 3-person party, Nintendo ultimately went with the far more tried and true scope and put craftsmanship quality underneath it instead (also, I don't think the plan was to make it true multiplayer like SoM, which was also another major source of that game's collision detection issues).