Prison arc from season 12 didn't mean much. It was an unoriginal and recycled storyline stretched out over the course of 10+ episodes. More than one recycled storyline, actually. Main character being framed for murder was done before and done better (in 2x12 "Profiler, Profiled" and in 11x22 "The Storm"), and Reid being tortured/miserable/in peril was also done before and done better (most notably in 2x15 "Revelations" and 11x11 "Entropy"). Lots of things simply didn't make sense (such as Reid being placed in prison rather than in jail, Reid not being fired from the FBI, and Derek not being informed about Reid's arrest and trial at all, not to mention an apparent lack of media interest in the case of the FBI agent accused of murder and drug trafficking; which, to tie in with the complaints #2 and #3, would have led to Reid being fired before the trial was over, and to Derek finding out even if nobody from the team informed him). Realistically, the case should have been solved within days, anyway, since Lindsey Vaughn left a fingerprint and DNA evidence on the crime scene. That was conveniently unknown up until the season finale. The only good thing about it waa the twist revealing that Cat Adams was behind it, not Peter Lewis... but by that point it was too little, too late. That arc revealed nothing new or interesting about Reid, and, if anything, they made him do dumb and reckless things he never would have done (such as going to Mexico and buying illegal drugs without even telling anyone from the team). Most of the fans were getting tired of recycled plots/story arcs and Reid being tortured/miserable way before season 12, and Reid's prison arc felt more like an insult, or, at worst, final nail in the coffin. It was a pathetic attempt to pull at heartstrings by (once again) torturing the youngest (and, arguably, most emotional) character, and also a cover so Erica Messer could say (if confronted with any complaints on that front): "See, we haven't forgotten about Reid after all, we still write storylines for him..." but everyone could see through her bs by that point.