I agree with a lot of what was said by the OP.
Spoilers galore ahead! Be careful.
I binge watched the whole show around two years ago and overall it was a great experience, though there is a pretty obvious decline in quality from Season 3 onwards. As far as I understand, Season 3 got hit by the 2007-08 WGA strike, which sucks because the starting point was actually cool (I mean, it starts getting a bit far fetched that all of them happen to be in this other prison, including Mahone and Bellick... but still, this is a show called Prison Break). But yeah, that season sort of came and went... and then it feels like Season 4 was left to deal with the resulting chaos, and it was a bit weird compared to the masterpieces that were 1 and 2. Still enjoyable overall and I liked my time spent with the show (including The Final Break). Only thing I really disapproved of was the last scene of the finale, which was all of a sudden and... unnecessary?
Then came Season 5, and after watching it, Seasons 3 and 4 are kinda better when compared, lol. It had a really strong start and it seemed like a media return that was bound to success... but then the storyline started to falter, and it all went downhill very fast. There are too many silly decisions in the writing and it really requires you to turn your brain off for a moment, otherwise you won't enjoy it. I wish they made it more about the prison somehow, but it evolved into this game of cat and mouse with a villain that was completely underwhelming and had dumb motivations. Things like Sucre showing up out of nowhere on his freighter... Michael being pretty much a God that knows everything (greatly exaggerated compared to past seasons) and then there's the whole story of T-Bag... no reason for that prosthetic hand at all, and he has a son who was half the world away, yet Michael found him... I don't know, it just didn't cut it for me.
Overall, I'm still OK with the Prison Break run, and the main reason for this is how incredibly good Seasons 1 and 2 were. I like the end scene, and despite my issues with the season, it fixes the problem I had with how it had ended before this return - giving it a better ending after all they went through. It was good to see the characters again, but the storyline felt more like fan fiction at times.
I felt this way when I watched Batman v Superman. Yes, I liked it - but walked out of the cinema to a massive amount of people that hated it (I didn't see anything critic-related before going). It felt weird, especially because I think there was a lot of "bandwagon" hate and I feel like this is happening a lot, especially with the bigger blockbusters (not meaning to disrespect people that actually didn't enjoy it for actual reasons, but I think it can't be denied that people jump on the hate/love train lately, as if there is this huge agreement to like or dislike something).
Honestly, voicing your views on media should never lead to an argument. If anything, it could lead to some discussions that make us all open minded - I swear I've seen negative reviews of BvS with points I agreed with, that made me think "actually, yeah, that's a good point". And I've seen a lot of good comments about Prison Break Season 5 as well. It makes me sick that on social media these days, if you like/dislike something, someone will likely fight you for it - but it's up to us to avoid that staying genuine and civilised, lol.