You might be right about this. Currently, it just looks like a mess of colors. Perhaps in 3D it works better.
The part that really bothers me though, is that I have no idea what the enemies look like. They don't have recognizable shapes or easily discernible silhouettes.
Provided you will probably want to shoot most enemies from the greatest difference, due to the 3DS's low resolution screen, enemies will just appear like a jumble of twitching dark pixels.
For example, look at this screen shot, and tell me if you understand the shape of the enemies on the screen.
http://e3.nintendo.com/_ui/images/games/3ds/codename-steam/screenshot7.jpg
Bugs don't make good enemies if their silhouette isn't easy to understand. It's more "tactile" and fun to shoot at a bulbous objects.
I'd rather be shooting at those big green blobs in the screen shot