I really enjoyed Secret Invasion (I only read the main series) as a whole. Yu's art was absolutely gorgeous, colorful, packed full of characters. I just want to wallpaper my walls with all the panels of this comic. The story was huge, epic, and action-packed with so many shocking plot twists.
My only complaint is that more heroes should have died. The Wasp was a prominent death to be sure but did ANY other major character die in the entire run?
The ending twist was pretty cool as well. I don't read any other Marvel comics but I read articles about them, but this is a very promising lead-in to future stories.
I was very confused to see Namor and Emma Frost in there, I thought they were good guys.
I think the nicest thing about the ending though is making Iron Man into the pariah. It's about time he got his comeuppance for the Civil War. And if the US military refuses to use any Stark Tech, wouldn't that bankrupt his entire company?
One thing I never felt was sufficiently explained was the Skrull's motivation. "He loves you", God loves you... I felt like this was leading to some huge revelation that never happened. I think read somewhere that in the Hercules tie-in they found the Skrull God and killed him... is that what the entire "he loves you" thing was based around? There wasn't any mention of this in the main series.
Also as a Marvel newbie, how the hell is Norman Osbourne a member of fine standing in the eyes of the US government, that they would put him in charge of the Thunderbolts and Shield-Deux? I just read a recent Bendis comic called The Pulse where Osbourne was arrested and convicted for killing a reporter as the Green Goblin and this was from back in 2004 or so!