Not that good
Sadly, it isn't that related to Metal Gear Solid, apart from the fact that Metal Gear appears in it as the powerful killer pokemon. If you want to make it more MGS like, you could perhaps add more sneaking and stealth kills, but that wouldn't really fit too well in the world of Pokemon.
Other than that, improve the quality of the sprites and special effects that you use, especially the special effects. You could also add voices as an option too and perhaps improve the plot a bit. Try making it feel a bit more like the actual Pokemon game as far as text and the battle screen goes too.