The more flexible a system is, the more expensive it generally is. At no point have you mentioned cost and/or quantity. These are a major engineering input.

What you're describing is a micro computer, not a micro controller system! So, something like the LPX21xx series is probably not really suitable. If someone came to me with such a spec, I'd be looking at someone like Advantech and buying their modules. If you want 4-20mA? ADAM module, a/d? ADAM module, digital i/o? ADAM module and the rest can be done with a panel PC or the like. Write your code under Windows. Before anyone goes berserk over the choice of Windows, if the OP can get it going under Windows, he's got a better chance of getting it running under anything else. Besides, Windows itself is quite stable, just don't let the users fiddle with it!

In all, I doubt if anyone can give you a concrete answer to your problem. Ten engineers would come up with ten different solutions, each with their good a bad points. Firstly, build something that works, then you'll have a better idea of what to do next.