Pietersen has fallen out with people his whole career though. Watson was the captain in waiting had Clarke not survived the Ashes summer, so it's not surprising some media reported a rift.
In a straight "him or me" ultimatum Pietersen will win and Flower will be gone every time. Right now Pietersen finished top runscorer while Flower was in charge of a side that lost 5-0.
All of the younger pundits out there - Vaughan, Tufnell, Harmison etc - are saying Pietersen should be in...