I thought season 5 was probably the weakest actually, although it's been a while since I saw season 2, and I'm waiting on my mate to return my first series box before I watch them all again.
I just thought the newsroom characters in season 5 weren't as well-rounded as everybody else was. Shifty Reporter Bloke was always shifty and naughty, Goody Two-Shoes Sub-Editor was never anything but the voice of rightness, and the Dopey Senior Editors were never humanised beyond "often makes the wrong decisions." The strength of the Wire for me was that no-one was ever 100% good or bad in it, but I guess only having ten episodes for the last series didn't give them enough time to do this for the reporters too.
I just found the shipyard workers "plight" really quite dull. The head honcho of the docks was a great character though, and so was his son Nicky or whatever he was called. It just annoyed me, because I loved the whole Stringer/Avon storyline, and wanted it to continue asap, so Season 2 came as sort of a barrier to that (although they pop up occasionally in Season 2). 5 had some good moments in the actual police which is why I liked it. Agreed, the newspaper storyline wasn't my favourite, but it wasn't bad.