They decided to do a "soft reboot" of the main storyline and start the All Hail Megatron series. Unfortunately that reboot forced Simon Furman to take the loose ends of his story (the first time the legendary Transformers author was allowed to build his own mythos instead of working on an ongoing story) and basically shove it all into the last few issues with some quick fixes. It was a real shame, since I absolutely loved the series and he was building up some really epic storylines. Alas.
All Hail Megatron was supposed to follow the continuity of Furman's series as well but it was obvious they weren't even trying.
He still writes quite a ton for IDW (the day Simon Furman stops writing Transformers will be a sad one indeed), he's just not responsible for the main storyline anymore.