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It's certainly not as easy to program or as well supported. You can use MS on anything from a chainsaw to a V12, program and tune it yourself using open source, free software. It's fully documented, can control the injection and the ignition, supports user switchable dual maps so you can implement your own 'sport mode' and 'economy mode'. People have even used it to drive common rail diesels and gas injection. I'd like to see you persuade a Jimny ECU do half as much!
I think people view what they have the most experience of as the 'best'. At the weekend I had a conversation with an Omex 'guru' who thought MS was rubbish - but had never actually used it. He certainly had more tuning experience than me - but couldn't really argue on cost or ease of programming and free software.
I'm sure each has it's advantages - so it just comes down to what you're used to.
The stock ECU has a dual core processor with the primary timing functions handled by a timing processor unit that runs autonomously. It means that it runs much tighter control loops ie better fuelling and timing. The code on the MS is based on the old 80s GM ECUs and is considerably less efficient, it also doesn't have any of the back up algorithms or default settings of the stock ECU.
MS is also lacking in I/O compared to a stock system which makes it difficult to pass emissions on a modern vehicle. One example is that the Jimny uses a unipolar stepper motor for the EGR but MS only supports a single bipolar stepper motor.
The advantage of the MS system is its ease of tuning but the stock system does contain a bootloader which allows simple code changes. There are a number of free programmes that can be used to modify the mapping
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