I think there biggest issue was just starting the show in the fall. They had to have known going into the year that they would have this massive twist in April that they had to work around. Why not just wait until the mid-season mark in January to debut the show so you aren't treading water for your first 6 months?
I hope they clean up their story plotting a little bit for season 2 in the absence of any movies to work around, although Buffy tended to have seasons start slowly as well, so maybe that's just a Whedon family writing weakness. Looking at some articles about ABC's fall upfronts this week, it sounds like SHIELD is going to take an extended break at mid-season with "Agent Carter" about the early days of SHIELD in the 50's with Cap's old girlfriend airing in it's place for 13 weeks. If I was writing the show and that was the schedule, I think I'd just split the season into 2 completely different stories to keep the plots moving fast and cut down on case of the week filler episodes.
Interesting I thought the Agent Carter was going to be in the present and star the girl who played Sharon Carter in CA 2?