Go read the MegaManual first....

You'll likely find that version 1 is all you need at first. It is relatively inexpensive, it certainly is a known quantity that is well developed and is, IMHO a great starting point. Going to version 2 is a relatively simple upgrade that can be accomplished later. Once you get the tuning close to where you want.

The key thing about MegaSquirt that most seem to ignore is that you have to be able to spend the time tuning and diagnosing it. Adding a bunch of features, etc to it makes it harder to tune and diagnose for the person new to the system. Follow the KISS solution and add features as you need/want.

For me, until they get sequential injection going, I'm going to stick with Version 1 or 2 since there isn't much to be gained on a fairly simple turbocharged 4-cylinder in a rather simple car.

Eventually for a turbocharged car, you'll want to add the capability to tune things more closely with more resolution. So I think MSnE might be a good idea once the rough tuning is done. Adding spark knock capability is also a good idea for long term reliability. Past that, its just tuning, tuning and more tuning!

Good luck,
Stefan