A lot can be done with Unity, it's a 3D-engine at heart but you can make 2D games with it as well (which we are doing). We've been planning on using it since the very beginning (so around 3-4 years). We've only started demo'ing a couple of months ago, though.
Right now, we're doing many things. One person is already making small demos. Our character can already attack (normal attacks), wall jump, jump, move and crouch (though, we still don't have the right animations for some of them) so the foundation has been laid out in terms of gameplay. Of course, the sprite we're using is something we made randomly and won't be used in the actual game. These demos are made to test things so that we already have a foundation when we have more assets further down the road. We've also started working on the artstyle and developed, what could be, how the sprites will look in the game. They're not really pixel-y right now, though. They're actually quite detailed (a la Kingdom Hearts Chi) but we haven't implemented these sprites yet so, depending on how difficult they are to animate, we'll "degrade" them appropriately.
Aside from those things, we're also trying to think of how we'll approach cutscenes. For now, it'll be something along the lines of the Persona games and Kingdom Hearts CoM, where you have the character art conveying the emotions of the characters and the sprites in the back play out the scene. But this is all still pretty rough so I'm sure it'll change as we continue development.
Of course, this is just us making these things. With the number of peopel we have now, we're not able to do everything for the game ourselves so we still need more people on board to be able to finish this project