I think we should try everything.

I'm all for the 3D idea, and in an ideal world that would be amazing. But while that is going on, why not use RPG maker? Why not make a 2D sidescroller? After we've tried different things and evaluated ourselves, we can figure out what works on the short side versus the grand scheme. This is, after all, an open-ended project. Though the sky is the limit, we are essentially building from the ground-up.

A friend of mine and I are planning a 2D sidescrolling mini Flash starring a servbot, for example.

The goal of this project is to revive Megaman Legends 3. That's why we're trying to make it as closest as possible to the original (or even better). While a spin-off like a 2D sidescroller is also a good idea, it's very far from what we're trying to achieve.
I look forward to that game, though

Keeping it like the original is the main goal. The main audience for this game seems to be the fans who played the originals so making a 2d version just wouldn't be a Legends game to those long time fans. Yes a 2d game can be just as fun but it's just not Legends.

Whatever the case, we'll need to evaluate the skill level's of each of the team members before deciding on what we can do initially—then we can focus on improving our skills and understanding of how to make a Legends game, and start testing things out, such as game mechanics and concept designs. That's what needs to happen—if we just need to try something out in 2D or an isometric perspective, then it'll perhaps be an option when such a context comes.