We had this problem on a feature film that I was AD'ing at the time. It was a student production and by the time pre-production was over (principles from each department had started early, around the middle of August), it was already mid-September. We knew there were going to be a lot of exterior scenes, but there were also going to be more than a few interiors.
What we finally decided to do, since we weren't shooting in order and the weather around us would create horribly different visuals (it was supposed to be set in the summer, so we had to avoid leaves turning and falling as best we could, but we had to avoid snow altogether), was to shoot all of the exteriors first, and in about two weeks. Then, we could shoot the interiors at our leisure on weekends.
The only real problem with this is anytime there is a large window during daylight that might give your season away. Also, we shot over a two-and-a-half month period, so we always had to be on our actors about not getting their hair cut, not losing or gaining too much weight, and trying not to change their tans and facial hair. But, we decided, it's a lot easier to control actors than it is to try and control the weather.
And we always had cover sets, so that if it was raining or the weather was against us, we would be able to shoot an interior scene and try and pick up the exterior at the end of all the exteriors, instead of waiting for the spring. This resulted in a couple of continuity issues, but nothing that was insurpassable.
