The issue is very specific structures, like the way nukes are handled in general. If nukes are enabled, the AI will throw them at you constantly. However, your own anti-nuke silos are incapable of auto-building anti-nukes, which was possible in the first game. The result is that you have to periodically go back and check your silos to make sure there's anti-nukes. This becomes increasingly frustrating when you consider that "strategic launch detected" also sounds for friendly nukes, so if you've got a friend you can't even count callouts. If you turn nukes off, then you lose the anti-nuke silo, which for most factions is ALSO the anti-tactical platform, thus preventing you from dealing with cruise missiles or missile tanks, which will wreck your shields and then wreck everything else.
Plus they took an inventive and challenging resource system and reduced it to 1990's level of infinite stockpiles, removed the ability to let one factory aid another factory, removed the ability for one engineer to aid another engineer, and generally took all of the very nice and 'ease of use' features and discarded them for no readily apparent reason.
They also got Square Enix to work on it, which if you ask me is just taking a perfectly good lobster dinner and asking a redneck to deep fry it and slather it in butter. Sure, it's some sort of tasty, but you've really just ruined what could have been incredible.
But that's neither here nor there, maybe. GPG did produce a mediocre sequel to something amazing, so as far as I'm concerned their track record has been 'it gets worse as the company gets older'.