I've been playing this on and off, some thoughts:
1. The game closest to this one is not metroid, is in fact Wonderboy 3: The Dragon's Trap (One of the finest games in existence). While it doesn't have the whole RPG-esque armor/item system, it has the whole core exploration mechanic that is sectioned off by virtue of the player's current abilities. The player has a bunch of different forms with the same base gameplay, but abilities that really change how they play (one form can climb walls, one form can fly, one can do a huge arcing strike, one can swim, etc). If you haven't played Wonderboy 3, I recommend you try it.
2. On that note, I like how the sword is essentially a 'heavy' character, while weaponless is 'speed' style.
However, this is a sonic game, and I think what you consider 'basic gameplay' is off from what people expect. What I mean is that right now 'base gameplay' is considered a character that can jump. When he has 'sonic moves' equipped, he gains spindash/rundash/spinjump and becomes speed-type. When he has sword equipped he gains sword strikes/ability to break sword walls/sword wave/etc.
I think the 'basic gameplay' should be Sonic's Sonic 1 moveset, at minimum (if not Sonic 2). This means, regardless of equipment/setup, Sonic has spinjump/spin attack, and probably rundash or spindash. Then the sword gives him sword waves, ability to break sword walls, etc on top of that, while perhaps equipmentless offers things like insta-shield and what not. Equipment should feel like it's adding power or gameplay, rather than exchanging it (That statement is completely opinion).
3. Is there a save feature? I haven't run across yet if so. One thing to keep in mind about exploration-style games is that they tend to take much longer to play. As someone with lots of life-obligations, being able to put this down and pick it up again later would be *very* appreciated.