It's all about the expensive systems here. Some will say "you get what you pay for" and not know what they're talking about because they have no experience with it. It has its quirks, but it is just as reliable and 99% as tunable as the expensive stand alones, plus the added ability of if anything breaks (which I have NEVER had a problem with the MS itself, just configuration), I can easily fix it myself. I run a Megasquirt on my turbo Saturn and ran one on my DD prior to the IS. I don't see any reason you can't run it on the IS. In fact, I might run one when I turbo the IS just to say it can be done.
In my experience, I like the MS better because I have total control over everything the system does. I can even modify the micro code if I need to. If it's support you're looking for and you don't want a system that is for the most part Open Source, the MS isn't for you. If you're in to doing your own thing and don't mind troubleshooting your own issues, and only need the support of the MS forum when you need it, go for the MS and save yourself some money.
It only has a "bad rep" because people that have no idea what tuning even is jump head first into a Megasquirt expecting it to be as easy as an expensive stand alone. "Plug and Play" if you will. It's not. So people hook them up wrong, configure them wrong, or just plain are retarded and they blame it on the MS. 100% of the problems I have seen with the MS are user error.
Nate