There might be some animation improvements to be made, but aside from that, it's a great start and an eye-opener for Capcom if they really wanna remake the MMBN series in 3D and put Andrew Francis voice into action among other actors.
The Mystery Data could use some gleam/shine, and they could use what I like to call the "retro TV blip" animation with a small beam upon getting the data from it (or when MegaMan's "data get" window appears.
Another thing is uh.... the school boy's mouth looks like he could shove a whole backpack into it. Maybe make him look a bit more human? I know you're trying to stick to the original art, but some mouth and facial shapes are a bit... wonky or unnerving. Taking inspiration from the school girl face and making it a bit more boy-like (similar to Lan's face) might do the trick. (Maybe something similar to how Sonic's mouth moves to the side for some characters like that school boy could work too... and maybe in instances where the mouth looks like it's mirroring and forming a triangle at the middle of the lip.
In addition, the mouths on Dex, Lan and MegaMan, especially Lan and MegaMan with the disappointed/sad expression is... weird.... like it's mirroring and looks like triangles instead of actual mouths, especially when talking. It might be a bit difficult to fix with the model, but having a few more bones and subdividing the mesh around the lips might work wonders for that.
The Navi Chip effects could use a bit of a camera/animation revamp for a bit of a smooth transition instead of clipping from one position to another in addition to Roll's head ribbons being capable of whipping about like she's turbo-slapping the opponent could work. In addition, having "head target" points for the Navi Chip's corresponding NetNavi to look at and approach might allow a more dynamic feel to the Navi's focus on.
This "head focus" can also be used for Lan or MegaMan to look at nearby NPCs when in a close enough range while passing by with some neck/head constraints to avoid some nightmare fuel that the "owl neck" head-turns can turn into. Constraining the neck-turning bones to only allowing 90 degrees to the left or right on the Z-axis and allowing the eyes to lock on and shift to the limits of the sclera might allow for dynamic head/eye tracking. It's a difficult and subtle touch, but one that many might appreciate. (Twilight Princess and BotW made me think of the head/eye tracking idea.)
All in all, a great remake.
Scores:
10/10 for the mechanics
6/10 for the character model
8/10 for character animation
8/10 for the environment model/animation
7/10 for battle animation
Summary: Some animation and modeling quirks here and there in need of sprucing up or revamping, but great remake all-in-all. Capcom could use you on their team for sure if they can get their heads out of their butts and make some epic remakes with your help.