The short version response: I'm not sure I'll watch the second season.
I was one of the people who was pretty excited by Marvel's Agents of SHIELD before it showed and pretty underwhelmed by the first few episodes. So I've only gotten around to watching the first season now, after I heard some reports that it really shaped up with some Whedon-esque twists later.
Uh, well, I'm glad that some people like it.
Now, I really don't want to perform hate on a bit of popular culture because (a) it's not really worth it and (b) it's really hard to make anything, let alone make anything good.
So, what's the good lesson to take from this show? The big lesson is: don't hide your light under a bushel. Or, more concretely: if there's something that makes your work interesting, don't hide it under a long setup. As the discussants at Writing Excuses have said several times--even using Agents of SHIELD as an example!--if you're writing a revolutionary take on epic fantasy but only reveal the twist in the last chapter after writing the whole book as straightforward fantasy, you will have effectively (a) driven off the people who are interested in revolutionary takes and (b) disappointed the fans of straightforward fantasy who stayed with you.
In SHIELD's case, the big twist that really energized the show (somewhat) in the second half was the revelation that SHIELD was infiltrated by Hydra, which was tied into the second Captain America film. Even a hater like me can see some logic to holding off on that reveal, both logistical (the show needs to start with the regular season of shows, but the movie only comes out later); and artistic (the big betrayals will have more punch if we see everyone pretending to be good at first).
But, oh god, if you're making a show about, say, how a 1960s ad man is really sleazy, you don't do 10 episodes of normal ad life and then show him cheating on his wife in episode 11. You end episode one with that revelation.
Or, let's take Hitchcock's famous dictum: a bomb goes off at a table and blows up two guys--how surprising! That's good and sometimes good enough if all you want is a sudden, sharp surprise. But if you show the bomb and then show the two guys talking normally--suspense!
So, if I were doing a SHIELD show (which is unlikely on a hundred different levels, but go with me), I wouldn't burn 13 episodes of mostly blah adventures, building up pretty cliche characters and pretty cliche characters' relationships. Instead of having bland adventure guy and bland hacker girl build up a relationship only to reveal the secrets, I'd much rather show bland adventure guy's secrets from the get go. That way, viewers could spend the time realizing that bland adventure guy's blandness is a put-on.
I could point out some other issues (like that time that some guy gets magically killed over the phone, when the guy on the other end turns out not to be at all super-powered), but the second biggest lesson to take away here is be interesting. That's a little vague, but the show leaned heavily into some cliches, from "He's standing right behind me" to action-movie-style quips in the most inappropriate places.
Let's just all agree to write that on a card and put it over our computers: BE INTERESTING.