As mentioned before, if you can find someone knowledgable with tuning, that Megasquirt setup is the ticket in the dollor/capability ratio. The stock ECU CAN work but technology has come a very long way. I'm a guy that likes to tinker and tweek. So while i can pay someone for dyno time and a custom chip for say $400...I am essentially LEASHED to that guy for any changes to my combination. Physically...I have to got to him. With the Mega, FAST, BigStuff, and Holley (which if you can afford it...is effing amazing)...I may not KNOW myself how to tune it completely but I can be coached over the phone on my own laptop and I have the ability to make changes while I'm miles away from my "tuner guy" and eventually, I can become my OWN tuner guy. I think you get more accurate tuning as well in boosted applications with a MAP Sensor that reads boost vs. MAF that only reads flow. I am not a pro tuner and don't claim to be. Thats my $0.02.
The ability to pull over, whip out a laptop and make adjustments and keep up with your parameters on the fly is amazing. I have been spoiled with playing with a couple of my buddies Hondas that are running K-Pro and I am incredibly jealous that we do not having something as simple, not that expensive, and as user-friendly as it is (it is one of the big reasons I want to pick a newer model Honda). We are by no means tuners, but I can say that we took a base map downloaded straight off the internet, and played around with it and my buddy has been driving his K24 S/C'd hatch daily for months with no issue. We have a couple different tunes for strip vs steet (mostly just adjustments in rev-limiter, 2-step, etc) and it's been pretty fun to play with. I've played a little bit with datalogging with some older school setups on another buddies Talon but it was infinitely more complicated because it did not come with a help section and lots of online information from Google.