From a story perspective, Empyrean Age was probably the worst blow to the credibility of a long-running PF I have ever seen in my life. The things they did do, the things they didn't do, the vast opportunities missed - even a fundamental fix to the mechanics of factional warfare will not undo the terrible damage to EVE's story that EA inflicted. There's so much wrong with the story elements that I don't have the stomach to go into it right now, and the way the story was implemented - with absolutely no player involvement, mitigation or input whatsoever - was a vile, pathetic disgrace.
What irritates me most, however, was the things CCP didn't do. This entire story had the potential to get rid of CONCORD permanently, remove limiting factors, let the war have some real consequences, but no, CONCORD came back stronger than ever somehow. By having Sarum show up at the very last moment with her magical bullshit device, they missed a golden (harr harr) opportunity to seriously throw the Empire for six and explore the actions of a demoralised Empire once again robbed of the illusion of invincibility - and the brutal, cut-throat struggle between the Heirs to become the new ruler of an Empire that desperately needed strong, unified leadership. This isn't just me hating on the Amarr - no-one should have saved them. The Elder Fleet - or, in a perfect world, whatever came for the Amarrians - should have fucked them up, and good, repelled only by a desperate and costly last-ditch effort by the remnants of the Amarrian Navy. Perhaps they could have had Admiral Saracen convince the Theology Council to let him redeem himself by leading the charge against the invaders. Having the Minmatar victory be phyrric was a terrible mistake.
Don't even get me started on the clusterfuck that was the Caldari-Gallente storyline.