People really need to learn patience in tv. Not all tv shows can be great from the start, for very different reasons.
I actually think that the run-of-the-mill, average, mundane episodes in the beginning of the season might have been that way as a means to set the stage for the big scene at the end.
Think of the season like a roller coaster ride. The beginning is very flat, to build speed. The climb to the top of the vertical curve isn't particularly exciting, but is very necessary. It's only when you go over the tangent point of the curve that the fun really begins.
The producers have said they were working with full knowledge of what was to come in Cap 2, but had to be careful to build their plot without spoiling the bigger Cap 2 surprise.
We needed to see a more average, day-to-day operation of SHIELD to begin with, in order to build up the suspense and to work our way up to the point where things got interesting. This gives the story the emotional build-up it needs so that when the big moment came (Out of the Shadows and Into the Light) we would realize the full effect of what had just transpired.
Don't get me wrong, some of the early episodes were very flat, and I chalk that up to being the first season, and writers finding their grove. (Think of how bad Season 1 of Star Trek: The Next Generation was, compared to what followed) But, ultimately I think the writers wanted us to have a fair understanding of what SHIELD was, and what they do, so when they lit off the nuclear implosion, it would be that much more impressive.
As for this show getting a Season 2...I wouldn't bet against it. I think of how much universe building this show did, leading up to Cap 2, and what it is doing as the follow up, and I can't imagine anyone turning down the opportunity for an even bigger build leading into A2. Hydra is revealed, and the after credits scene in Cap 2 tells us we've only scratched the surface of how deep Hydra runs in the modern day. This is the perfect wheelhouse for Agents of SHIELD to work in, and Agents of SHIELD is the perfect vehicle to set up the circumstances that will bring Earths Mightest Heroes back together again.