Full disclosure, I'm a close friend of
@Shita-kiri_Suzume but I've read both series.
I think it's fair to say that a good takeaway from both Nagatoro-kun AND Uzaki-chan is that respecting people's personal space is pretty important. The former is a bully and the latter is a pain in the ass. Bullying isn't okay regardless of whether it ultimately leads to anything good and Uzaki-chan does need to respect boundaries more. That said I can easily see how people can find either character endearing and are willing to make excuses for them or suspend their judgment to enjoy their antics. But I think the criticism is legit in either case. If you find Uzaki-chan unbearable I don't blame you but I definitely see why she has her fans. (besides her obvious... err, front and center charm point)
If you've seen me elsewhere on Mangadex, it's usually in the genderswap genre. So I'll bring a bit of my native country's flavor here -- if you were to swap the genders of all involved, how much does the story change? Nagatoro-kun suddenly takes a pretty twisted air. A girl with no self-esteem being emotionally broken down by a popular pretty boy who can barely hide his disgust for her BL works. Whereas Uzaki-chan's story might even be more adorable -- an annoying, expressive loud little-brother boy who won't leave a grumpy large-chested girl alone, but whom inspires nurturing feelings from her.