This is Jerry Hoffmann from DIYAutoTune. I've got MegaSquirted cars I haven't touched in years, and still drive just great. I've got other cars that I mess with from time to time... the question is really "How long can you stand to leave the rest of your engine/exhaust/intake/etc alone?" The reason you have a standalone EMS is so you can tune your engine for the best performance with the combination of components you're running... change that combo, retweak for best performance. Leave the car alone, leave the EMS alone. I haven't touched my MR2 in two years. I did a mild retune on the Miata not long ago as I lost about 20whp when I put a cat on it, so I up'd the boost 2psi using the MS controlled EBC and dialed in the fuel as it was a bit rich on top, and it's back at the 253whp mark.
Just like any good EMS, they don't need to be messed with unless there is a reason-- if you choose to update to the latest firmware, or you modify your car further and need to fine tune, or choose to add a new feature like EBC control and want to dial it in, etc. If you properly tune a car and then want to leave it alone-- no problem. But how many of us do that? Most of us are tweakers... that's a part of the game. Standalone EMS systems like the MS give you massive amounts of control, but there is some level of complexity involved which is where the tuner shops make their money for those that don't want to DIY the tune. You can set it and forget it, or make a hobby of it, it's really your choice.... and in that respect it's no different than any other ECU, we just tend to have more hobbyists playing with MS's that other mroe expensive ECUs do as the pricepoint makes it more easily attainable and B&G really set out to build something that anyone could work with and learn from.
You could call me biased, sure, but I've driven long distances with no backup plan many times and never been stranded once due to a problematic ECU. I have made enough torque in that Miata that my co-driver destroyed the tranny at the track... so I guess you could say that a MegaSquirt could cause your car to make so much torque that it's tranny could explode and is therefore unreliable .
Jerry a.k.a. 'FoundSoul'
http://www.DIYAutoTune.com