My take on a few of your complaints. The Coulson one I felt was more than adequately addressed by other people.
Loki & Hulk - It's a comic book movie... and the scene worked for 99.9% of the audience. And Selvig and Hawkeye were powerless anyway, what could they do?
Thor's entry - EXTREMELY glossed over, one of my biggest complaints. They should've SHOWN it rather than TALK about it. But I got over it quickly once Thor and Iron Man went at it. And when Thor talks to Loki, it's made very clear that sending Thor took a major toll on Odin, so for a global crisis it's worth a go, but not exactly something Odin wants to go through say if Thor wants to go on a date with Jane.
Pepper - I loved how they restored the banter and chemistry that she and Stark had in IM and completely missed in IM2. Romantic interest was to humanize the characters more and IM is the biggest seller of the Big 4. They capitalized on IM's self-sacrifice towards the end by showing who he had to lose when he was trying to call Pepper, so that worked for me.
Aliens - Target practice, but that worked for me. The action scenes were still amazing and I couldn't care about creating more depth for the alien invaders. Another major complaint I have was the cop-out of how destroying their command center effectively killed all the aliens, but I got over that quickly too.
Argument scene - I put my take on that scene in my earlier posts, and I'm still not 100% clear on it despite having seen it twice. What I can determine (and confirmed by other people who've seen it) is Loki had Banner under a spell to make him lose control, but there's less consensus on the minor details surrounding that scene. Not sure if Loki's spear plays a role and was getting the rest of the room agitated, everyone clearly had enough beef to start fighting each other even without any magic involved. My take on Banner grabbing Loki's spear is because that was the closest weapon, not necessarily because the spear was making him do anything. Whatever people thought about that scene, what the audience needed to understand was Loki manipulated Banner to get him to Hulk out and that was all we needed to move on with the story. Banner then shows he has a good amount of control over the Hulk during the final battle, so his first Hulk transformation and subsequent mindless rampage was Loki's doing. I agree that this entire scene could've been fleshed out better to make things more clear, but the story moves on w/o any major hitches once we understand that Banner was Loki's play there.
BW-Loki - I agree that parts of this scene felt forced, but bottomline is we got to see how BW is manipulative and how Loki is much more deranged since events of Thor. The scene overall worked enough for me and I moved on.
Loki: C'mon, he's a GOD. How can Hulk even grab him (remember, Thor gets suckered by an illusion of Loki earlier in the movie?), much less beat the crap out of him? Why do Selvig and Hawkeye just stand there and let Loki touch them with his staff?
Thor arriving back on earth: At the end of "Thor" he was unable to get back to earth, watching Jane Foster from afar, but in this movie he's able to get to earth to get Loki back.
Pepper Potts: Not sure why she was even in the movie. She just had a few scenes with a few throw away lines.
The aliens: Forgettable, overly designed, mindless killing machines. Just boring.
The argument between the Avengers in the lab: seemed forced, awkward. It was unclear why they were mad at each other. Was it the staff, was it because they found out Shield's plans for the cube? The fact viewers have to wonder about the reason is a problem.
Black Widow bargaining with Loki: Man, that was just hard to watch. It was far from convincing.
new Hulk movie in 2015 because of fan reactions on rufallos performance !
