This is a very simple hack idea, where the trainer (you) is a Mewtwo, rather than a human trainer. All sprites dealing with the player (trainer card, in-battle back sprite, overworld sprites including bicycle and surfing sprites) are going to be changed over to those of the in-game Mewtwo sprites. The scripts will be changed over to reflect you being both a Pokemon and a trainer. Examples include "Aren't you a cute Pokemon--AND a trainer, besides! Let's battle!" and "I've never faced a trainer who is also a Pokemon. This should be fun!" Trainers will also have kinder words when defeated. Examples include "Wow! Despite being a Pokemon, you are certainly a skilled trainer!" and "Being a trainer who is also a Pokemon does have distinct advantages, doesn't it? Good job!"
As a young Mewtwo, you are naturally very intelligent and also quite curious about EVERYTHING. You quickly learn all there is to learn at your home laboratory (your "mom" is actually the scientist who created you, but she's very nice toward you and nurtures your burgeoning adventurous spirit), and therefore are asked to seek further "education" by adventuring all over Johto and Kanto, in hopes of achieving your full potential.
Of course, along the way, you'll meet Professor Elm, who will tell you "two Pokemon are better than one", and offer you a choice of three starter Pokemon (the same Chikorita, Cyndaquil and Totodile normally available), and he'll ask you to walk with them, rather than hold them in a Pokeball all the time. Naturally, you think this is the coolest thing ever--being able to help train a fellow Pokemon, and be able to TALK to them (yes, as a Mewtwo, you'll be able to understand what the other Pokemon are saying).
UPDATE: I've already ported over two of Mewtwo's HG/SS walking sprites onto the player trainer's walking/standing sprites. I've even created additional sprites for the player's standing sprites (normally, your walking Pokemon is always moving, as if walking in place; therefore there are no actual standing sprites for it).
Additional tweaks to the rom will include having the Fly command available from the start (and is one of your default moves), and also being able to access the PC system at any time (by pressing START). Yes, I know that Mewtwo isn't normally capable of learning Fly (or Teleport, for that matter? What gives? The guy's PSYCHIC!), but I will have him be able to do so to make navigating throughout the in-game world easier (and faster). Of course, you'll still have to actually walk to places you wish to fly to later (in a sense "adding" them to your Town Map).
I found out what was wrong--you STILL need .NET framework 4.5, despite the fact that you advertised that you only need .NET 4.0. Not sure what happened, but I downloaded and installed .NET 4.5.2 (the latest version), and your program now works. However, I would suggest using a drawing program such as Paint.NET or IrfanView (both of which are available for free) when editing sprites. I even whipped together a few extra portraits for Mewtwo, using a simpler color scheme, and giving him a younger, more friendly appearance (your character IS a kid, after all, before becoming a Pokemon).