I never got any indication things were headed that way. Saw a lot of people online running on the assumption that it would happen though.
What, you missed the whole "SO" setup, the sharing and caring about their hard childhoods, the training sessions that led to Ward wrapping his big, strong arms around Skye, the many moments of awkward flirting and snarking, etc.? Skye and Ward have been getting the big push since their second scene together in the pilot. The two of them shared most scenes after that, up until the big reveal of Skye's treachery in episode 5, after which Ward noticeably cooled towards her. People have considered them an inevitable pairing because the show presented them that way.
Happily, the timely intervention of sexy Agent May has sunk that ship, at least for the moment. Something needed to slow it down. The fact that the May/Ward thing is so unexpected is a big bonus as far as I am concerned. AOS needed a kick in the ass to shake things up a bit. The writers papered over the problems that Skye's betrayal should have caused within the team, so strife had to come from some other source.
This relationship has the added benefit of keeping May out of the sexless, maternal older woman trap she might otherwise have landed in. Ward benefits as well. He is suddenly much more interesting than he was before, not to mention sexier. Brett Dalton has some charisma and range as an actor, which wasn't apparent in all the time he spent in Skye's orbit. They have actually succeeded in making Ward a more likable character after a rocky start. Even his scenes with Skye are tolerable with the cloud of his affair with May hanging over them. When everything comes to a head, I'd love to see the two of them blow it off while Skye goes ballistic, FitzSimmons are confused and Coulson is very, very disappointed.
