I really hate to be the guy on the other side of the fence from everyone, but I have to put my foot in the door for a sec.
First of all.. HURRAY! WE CAN STOP BLAMING NOTCH! He has officially made Minecraft Jeb's game! So Jeb pretty much has the final say on anything that happens to minecraft... boy I sure hope he DOES pull rank if Notch wants to do something stupid.
Okay, got that out of the way. As for Xp and enchanting... look... the game has NEVER said "This is experience" "This number is what level you are", people have only come to associate them with that because Notch made mention of it (Not even sure when, tbh... prolly E3). Anyway, the game doesn't say "XP" and it doesn't say "Levels". When I first played with them, I did what I did for ANYTHING new in minecraft... I made up my own explanation for it. And the number obviously meant I had accumulated quite a bit of these things and was there to give me a good indication of how much of this "stuff" I had. I mean, seriously, who else here made up a reason for why they had to hide in a hole at night because there were monsters outsi -- MONSTERS?!? Why are there monsters outside?! I dunno, probably because of blahblahblahbla-- See what I'm saying? The game doesn't elaborate on any of this. I was far more entertained by my own explanations of the surroundings than I was by ... whatever everyone else thinks of it.
What should we do about enchanting? Leave it. If someone was stupid enough to enchant their quantum suit, I hope they get Protection... boy how useless would THAT enchantment be on a quantum suit? Yeah, let's consume EXTRA charge to REDUCE DAMAGE!! That'll show those IC2 devs that I know what I'm talking about! Uh huh... whatever. Point is, enchantments don't come off. And you're worried that people will be making super uber equipment? So what? The quantum pieces are PERMANENT. If they enchant a quantum suit piece, they're running a HUGE RISK of having to scrap it and make a new one to try again!
On the other hand, instead of gambling away their hard earned soul-power-of-the-damned and hard earned Iridium, they can pool into researching and maybe having a CHOICE of upgrades for their suit.
I see this as a win-win! With the not-so-technical, you're gambling... a lot. With the tech, you spend extra time, but win out in the end.
As for potions... leave them as well. Potions are temporary, technology is forever. Potions would be a waste of materials next to technology, but a good alternative in the meantime until you can grow that technology.
I think a BETTER question here would be "What to do about blaze rods?" These things are FARMABLE FUEL FOR FURNACES!!! They are also technically a source of HEAT, so if they stick around, I better be able to feed these things into my geothermal generator! If not, a normal generator at the very least.
Yeah.... super post FTW! That was my 8 cents