The PE is a much, much nicer setup, as you say- the only thing that I'm a little uneasy with is the software. I haven't experimented with it a ton, but from what I've heard from the previous users, the software is quite a time to deal with (even in comparison to a microsquirt) and having an injector open time table instead of a VE table is a bit convoluted for something like a standalone. Thankfully the calculations (VE > Inj Time) aren't all that terrible- many of the factors stay constant as rpm and load change, but it's something I'd have to do a lot more research on. Regardless you're right, and I don't think my incompetence with ecus like this should be a reason to use a worse bit of hardware, and considering the MS is more likely to get taken away, it is indeed the better option.
I'm spoiled in that I currently primarily work with a MoTeC M150 where almost everything is...well, as you'd expect. At least for the engine tuning side of things. But a MoTeC is quite a ways out of reach and definitely over the top given the car looks the way it does