The biggest problem with NEM is that it is dramatically arbitrary. Why is Picard goofing off in a car in the desert without checking to make sure the local sentient species wouldn't be able t find them? He feels like it. Why did Soong build another android like Data and not tell anyone? 'Cos. Why is Shinzon so fixated on Earth that he wants to destroy it even though the homeworld of the people who actually abused him and oppressed him was Romulus
? Because Humans.
When characters make choices whose motivations feel unreal or incompatible with what we know of their personalities, that's a major problem.
The other issues are all very minor compared to that.