I've been waiting for this beta, being as I am rather fond of the Battle Network series. I've seen this attempted before but they didn't get as far as releasing anything at all, so you're already winning on that front. Anyhoo, having played the beta, here are my thoughts:
First off, this is way better than I expected it to be. I can see you've put the effort into creating that MMBN feel, and the super-deformed FR-style sprites work really well (the reworking of the FR old man into Dr Wily stands out for me, although Dr Hikari maybe needs some work). The Net Navis don't look horribly out-of-place in the real world, it's all consistent while at the same time making the Net clearly different to the real world. The only thing that would really make things much more authentic is if you were somehow able to edit the circles you stand on in battle to look more like the grid squares from BN, but that's a minor quibble at best. Oh, and maybe Megaman's head should move a bit when he walks, the staticness of his head is a smidge weird.
As far as difficulty goes, I found that with the bare minimum of grinding, I found myself one or two levels above most enemies, and felt challenged rather than unfairly outclassed. Some earlier comment said the Mega Buster might be took weak. It's not, not with STAB anyway. Besides, it's supposed to be weak, it's the bleedin' Mega Buster. Just so long as it's not Constrict weak, we're good.
I arrived at the Mettaur2 before I learned Heat Gun and was still able to beat it with some effort and a few BusterUps, for example. Even without heal spots at the start of areas, the amount of meds you're given should see you through. That said, Protoman decided to just spam nothing but Swords Dance and Agility when I battled him. I imagine I'd be having a rather different reaction had he 2HKO'd me before I could do anything. Maybe lower Swords Dance to BusterUp for that battle? Also, I have a personal dislike of using evasion boosters to turn battles into luck-based rather than skill-based affairs, but got a laugh out of it being called Copy-Paste.
Oh, and you seem to have this thing about apostrophes, in that you've mastered the possessive but can't seem to use them as contractions eg. don't, can't, you've, won't. Might want to fix that. And by might I mean 'please do.'
Overall, this is a great first beta. I'll be keeping watch on this as it develops, because it's got real promise.