The writing was good throughout.
The controversy was when they wrote stories that were paralleling current events. Two things especially come to mind. In the season where cylons captured most of humanity:
1. the humans (good guys) used suicide bombers to revolt against cylons and at the time in the real world suicide bombing used against US occupation of Iraq was being called terrorism. People didnt like it when shown the viewpoint of the other side.
2. Then cylons used torture to try to get information and were shown to be monsters, while many in the US were in favor of torture against anyone we call terrorist or might be a terrorist. People didnt like it when it was shown that what they were supporting was monsterous.
I didn't like those parts, not because I didn't agree with the stance the show's writers seemed to be taking (I did), but because it seemded lazily on-the-nose/topical - like they'd brought in writers from South Park to handle that. B5 did similar stuff, what with President Clark, the Nightwatch & the Ministry of Peace, etc, which had many obvious elements cribbed from the Red Scare era, Nazi Germany, etc - but I think those elements of B5 have aged much better, as a result of going with allegories that are much more universally recognizable rather than allusions to then-contemporary events.
It also doesn't help, admittedly, that all of that was during what was (at least, in my opinion) a low-point that the series never recovered from: the whole "New Caprica" arc. It started badly, with the random "1 year later" jump (which was so out-of-left field, I initially thought "wait, was the series unexpectedly cancelled & they had to shoe-horn an ending into the last few minutes of the season finale?"), it felt like it dragged on entirely too long (especially given the lack of lasting consequences), and its conclusion seemed to be one giant reset button - an excuse to get rid of the Pegasus because it probably made the writing more complicated, all of the changes to the characters being undone (Adama shaving his beard & Lee taking the cotton balls out of his cheeks... I mean "losing weight"), etc.