I am one of those who actually likes the idea of a *constrained* RNG based customization system. That said, I do see ways in which the system I saw on Tuesday night can be improved (assuming they haven't already implemented them).
-As your reputation with an engineer improves, then the amount of variability on lower class upgrades should be reduced (so a pilot with a level 5 reputation should get an almost guaranteed levels of upgraded stats for class 1upgrades).
-As an engineer does repeated upgrades of a certain class for you, then the variability should reduce. So, if your pilot has been getting numerous class 3 beam weapon upgrades from this engineer, then the next one he does for you should be less prone to variability.
-the quality of the goods used in the upgrade should impact variability. So if I bring an engineer a newly bought beam laser, & commodities obtained mostly from missions and/or stock markets, then that should be a less variable upgrade than a 2 month old beam laser and commodities I got from planetary/space exploration.
-A specific build (like a class 3 extended range beam weapon) should become a TEMPLATE that the engineer can build f9r you the same way, each & every time.....but only if you choose to save it. However, if you decide to get a new class 3 extended range beam laser blueprint recipe, then the old template is lost.
- with the weapons, there should be a button to select "no special ability". This upgrade would be cheaper, but would never give you a special effect. There should also be a button where you can choose to *aim* for a special ability. This would cost more, but give you a significantly improved chance of a special ability for your weapon upgrade.
I feel confident that, even if just the first 4 ideas got in, then even those currently opposed to the RNG approach might be OK with it

.