They've already done the "SHIELD is evil" plotline, I think it would be better if it turned out this organization was at least relatively good. I'd like to see them actually start to get along with each other after a while.

This is actually my big problem with the show: anyone trying to assert authority over someone else is portrayed as being a wet blanket (even when their conclusions are semi-rational), and nobody's willing to admit that said authority might be correct at least some of the time. For example, when Coulson tries to lock up Skye, she's completely indignant. This is despite it already being shown that just keeping her alive is a big risk.