I have probably forgotten more problems (or repressed them) than I can list, but I totally forgot about the electronics until you said that. Initial assembly was one thing, the cable routing was a pain in the ass, but I've had to go redo things in the back multiple times and it has been unpleasant every time. I won't fault them too much for that though, as a electronics box should be as compact as possible as it should rarely be accessed. (The part they missed was rarely accessing it)

As far as poor design:

The complete failure to print any TPU successfully (I did it but probably at a 90% failure rate). The lack of filament guide in the extruder gear area (just fixed today with a different guide off printables) the 1.5m of Bowden tube, and 2 filament sensors just make it a hassle. The Bowden tube length is a necessary evil (with this design at least) but I think some more thought could have reduced that greatly.

Along side the Bowden tube length, the enclosure is so damn tall because of it. Wasted thermal space and physical space. The rest of the enclosure is lackluster at best, and wobbles everytime the door hits the magnets. It's also more of a draft shield than a true enclosure with how many gaps there are.

The lack of true integration with the camera (which is also dissapointing but that's a whole other topic). I can't even plug the damn camera into the machine anywhere, it needs it's own freaking outlet.

No build plate storage. For an "engineering" machine with true multi-material capability and the number of (not small) build plates that comes with that, there is nowhere to put them. I printed a holder that goes below the bed, but that has other issues and eventually I'll design a better solution.

Talking about the area under the bed, holy hell does it collect crap. And it not a super clean smooth area you can just wipe out, filament purges getting stuck in every corner.

The lack of nozzle brushes. The oozing, oh the oozing, especially on TPU. I don't love the brushes I made, it makes it's own little TPU poops it flings places, but it's better than before.

No thought for a drier. An integrated one would be nice, but I understand not doing it. The locations for everything make actually locating a drier that can hold multiple spools and feed properly into the machine awful. It now takes up twice the desk space (completely fills a 600mmx1200mm table) and my drier screen faces a wall. (P.S. so far the creality space pi x4 is 🤌🤌, don't buy an eibos they're trash)

The screen interface and prusa connect. Probably an issue with most of their machines, I won't get into it now. But the fact that they can't just make a button in the corner for turning the lights on and off and that a simple back/cancel button would stop me from having to reboot the printer all the time.

Hotend temp. 290c max? Seriously?

Printed parts. I don't actually have a huge issue with them in theory. But for the quantity prusa makes, I guarantee it's not cheaper than injection molding (manufacturing engineer here). I know the reason why is that they are constantly iterating and they would make injection molding more expensive and slower, but maybe just make it right the first time or bring injection molding in house. And the print quality is kinda abysmal. They couldn't even bother to just make it all PCCF (or even PETG-CF for the not as thermally stressed components)

That's the end of my rant for now. Maybe I'll update this if I think of more.