Thats right, MS should. But in my experiance 8 out of 10 cars i have seen never run right or have some issues that the installer or maper has not been able to sort out. This doesnt mean it cant run right, as obviously it can. Your in finland (It says) so availibility of tuners for weber may be harder for you to find, hence why you chose MS. Where i am there is 5 good tuners with respected names that can map any of my cars for around £100-150.
Why is it more easy? All you need for a L6 which costs £50 is a coilpack driver which is £100. The L6 variant costs £1600 new which you can still buy direct from the manufactor. The weber setup is what most after market systems are based on anyway and other systems use the same sensors anyway like Pectel, Omex, autronic etc etc..
Great? So why it cars running MS still dont run 100%
This is another easy upgrade for a weber ECU using MSD chip. I would rather a decent name like MSD controling my closed loop lambda than a home made ECU..
Rad fans? Why involve fans to the management system when most cars that we would fit management systems to already have a great fan control system.

As for water injection pin12 from a weber ECU is the earth trigger for Wi. So all you need to do is set the ACT + the BOOST level for it to come on at, then if the pressure drop below x amount or ACT drops below X amount it switches off. Simple.
So out of intrest how much is the MS2 ECU that has been professionaly built and convered to stop dust and issues etc..
As said sequential injection is std on all weber ECU's which is far better than a batch firing system which is why even the best and fastest etc etc.. RST all use sequential cam sensor and cps setups.
Thats exactly the point. Why would you want to touch it once its 100%
My advise would be dont DIY important CPS and Cam sensors. Just spend £100 with a well know company to supply a 100% setup. For any system!!!
As said above the FORD fan control system on early cars are fine as long as you use the correct fan switch thermostat and liquid.
This is a nice feature available on most newer systems however if the car is setup and running 100% why would you want to be datalogin and messing around with the system. If you want to mess about then again MSD supply a fully mapable system for the Weber ECU that datalogs and adjust's etc. Why the "normal" person would want to do this is another question.
But above you said its autotune which is a bit mis-leading.
Any system from MS, Cossie, Pectel, etc etc.. would be reliable to drive and forget as long as its been done right using the correct parts.
By anyone? I doubt. For a fiver.. just makes me like the ECU less meaning it only has a fivers worth of parts in it..