Plus most people's experience with MS was with MS1 five years ago. Just because MS1 was first and is least expensive does not mean it is the easiest to use or best choice, in my opinion it's exactly the opposite. MS2 and MS3 are completely different and much more user friendly. Plus if you want it to run like stock or better, it's all in the tune, almost nothing to do with the hardware. An un-tuned Haltech will run just as good as an un-tuned MegaSquirt.
If you go with a programmable ECU, no matter what brand, make plans to visit a dyno. It is beyond me why anyone would purchase a programamble ECU so they can tune the engine for their modifications, but then never take it to a dyno to get it tuned and then bash the hardware / brand name when that's not the issue at all.
Call around to your local dyno shops and see what systems they are familiar with, that would be the best system for you to consider. If you find a shop that will tune a MegaSquit then your engine can run as good as with any other ECU but only as good as the tuner's ability, only for a fraction of the hardware cost. MS has evolved to the point with MS2 and MS3 where those that consider it a joke and only a hobby kit need to take another look.
http://www.diyautotune.com/racing/drag_week_2011_results.htmMany shops like to sell a particular brand of ECU and turn away the rest if you don't buy their product. Think about this, if you can tune a fuel table and ignition table, you can tune a fuel table and ignition table. Greedy shop owners will turn away a simple tune job because they're not selling you a multi-thousand dollar ECU and install job along with the $75/hour tune (or whatever their hourly rate is).
I run a MicroSquirt (MS2) based system on my engine and I don't care if someone gave me a Haltech, Motec, or one of the McLaren Nascar/F1 ECUs, I wouldn't trade my MS for anything. Remember it's all in the tune. I run a 16V with ITBs and LS1 coils, sequential fuel and ignition operation, individual cylinder fuel trims, reading RPM from a DLI GZE cam angle sensor unit in place of the distributor.
http://www.diyautotune.com/russ/itb-with-ls.jpgYes I do work for DIYAutoTune so view my bias as you will. I'm here to offer help and support should you need it. If you have any questions about MS or if I've made you raise an eyebrow, don't hesitate to give me a shout
websales@diyautotune.com and my name is Russ.