The only mention of Pepper in AoU is when Maria (Hill) asks Tony and Thor how come Pepper and Jane aren't also attending the party.
Tony gives an ambiguous response about Pepper 'having a company to run,'
So, with Pepper's absence, Tony's low-key response to Maria's question and AoU, narratively, being sandwiched between IM3 and Civil War, it's not a stretch to read Tony & Pepper as being broken up IMO.