QPE use MBE ECU, and sounds like they're giving them a bad name! I've used an MBE 967 on a track/sprint car for about 6yrs now and think it's great - bit it's horses for courses.
For a road car any aftermarket ECU be it Emerald, MBE, DTA, Omex etc, will all need a good bit of work to get it as well refined as a factory car, where thousands of dyno hours have been spent fine tuning for different driving situations etc. As Geo pointed out, the hot and cold start maps will take a long time to get right, due to the issues of cooling/heating a car repeatedly. Chances are remaps are going to be a little bit pricey, but you'll probably only do it the once.
For a track/race car when all your mainly concerned about is ignition&fuel map for high load sites and full power - then an aftermarket ECU makes a lot more sense, you're not as worried about hot/cold start, you're free to make constant tweaks to the map, and can use the ECU for other things like rad fan control, fuel pump control, traction/launch control, shift light etc. The MBE easimap software is very easy to use, and very handy for making small changes (which are usually required) to fine tune the little things that are taken for granted on an OEM ECU (idle, hot/cold start). But at the same time, if you start making serious engine mods - bit lairy cams, then having the ability to fine tune all that, with your own freedom, is going to be worth it.
The wiring loom for an aftermarket ECU should typically be a lot simpler - but it sounds like this is the bit that QPE have made a mess of, sounds like they've tried to take a complex OEM loom and merge it with an aftermarket ECU.