Kevin, there are a few key advantages I believe in the mcx kit versus the mpi, but with that said there is nothing really wrong with the mpi as it works just fine.
To start though the mcx fuel box is, well, awesome! It doesn't have any game boy buttons to push, any need to adjust or anything like that, you plug and play. It takes baro setting into account and alters the boost accordingly as you go up or down in altitude so you maintain a true 180 without having to adjust boost or fuel settings. With that said though turbos dont need a whole lot of adjusting as they are very forgiving in the fact they use a wastegate in the first place and use exhaust gas to spin. Now with a supercharger thats a whole other ball game, just stay away in my opinion unless your a trail rider and even then I dont like them.
Secondly, the charge tube is 18" shorter on the mcx versus the mpi and is internally cooled where as the mpi is just a aluminum pipe. This means quicker spool up and cooler temps. Not a huge deal but does make a difference.
They both use mitsubishi turbos so thats a wash however the way they are mounted in my eyes makes a difference. The mpi kit uses some type of diesel exhaust muffler or something, sounds different if you ask me, just a personal opinion though, I like the sound of the mcx better. I also like the exhaust coming out the back because it makes a great hand warmer and a little less tunnel ice when I compared the two . Again, on the mcx the turbo is mounted and welded to the header much closer than the mpi which means quicker spool, I think.
The whole electic pump thing kills me too on the mpi. Yeah it works but personally Ill take a mechanical pump anyday, no worries about it not working or losing connection or breaking a wire or something silly. I think they(mpi) went that way though was for easy installation purposes, as the mechanical is a little harder and time consuming to install.
With all that being said, there isnt anything wrong with the mpi kit as there are a bunch out there and all working great. If it were me and my money though and I was wanting to purchase one knowing what I do, it would be a mcx without a doubt. Now if I was looking for a new sled with boost, its hard to beat the 1500 dollar deal yamaha is offering for a turbo sled and would certainly take one.