You can exit the Floating Continent and go back to the airship once you get far enough into it. so there's no reason to worry about stocking up on items. There's a point where you see the airship floating below you and you're given the option to return if you want. Don't worry about losing Shadow on return trips, since he'll be waiting for you back at the beginning again every time you come back.
Also, all the items you missed on the M-Tek Research facility can either be bought or stolen later in the game, so you don't have to worry if you missed them.
The Genji Glove is also perfectly obtainable in unlimited quantities via Morph later in the game, so you shouldn't waste too much time trying to steal them from Dragons. Besides, you get enough Genji Gloves normally throughout the game to equip everyone in your current party if you want.
And you can't fight the Intangi in the WoR(except on the Veldt, if you encountered him in the WoB), so you have to beat him now. He's not really a "powerful" enemy, so much as a gimmick enemy. Know how he moves, and you can take him out with little trouble. He used to be easy as pie in the older versions where you could kill him while invisible with spells like Doom and such, but in the Advance version you have to slog all the way through his 32,000 HP the hard way.