That idea definitely can work if it's used the right way.
I have some suggestions. (You've probably already considered these,
but I'm just making sure you know that someone else thinks these are good ideas.)
1. Okay, so the basic path is from JFG, and the levels are Metroid-ish.
That would mean you're mostly using Sonic gameplay, right?
I'm thinking that it would be good to make the gameplay and level design
as fast as possible without ruining the Metroid part.
Maybe the levels could be big and have lots of speed sections
(loops, corkscrews, pipes), but still have rooms with items,
some places to use the new moves and items, and a few slower areas.
2. Putting the whole game inside a cave would make it boring,
especially if it's a Sonic game. Make lots of kinds of levels.
I'm making a Zelda game (Don't expect it to be finished soon.
It might not ever be finished at all.), and although it's mostly just
a third quest for the original, it has many different types of dungeons.
It has a forest dungeon (holes in the ceiling, small trees), a water dungeon,
a side-scrolling place like the SSBM level (narrow tunnels), and
(This is really weird.) some open areas that resemble Green Grove!
3. Let me make some (preferably 3-D) graphics for it! (pictures of polygon models, like in DKC,
or even real polygon models, like those blocks, fake walls, and logs from Yoshi's Island)
I'm getting pretty good at using this program, now.
(Yeah, that picture is sloppy. It only took a few minutes.)
