Totally agree.
I thought this WHOLE idea tanked when the Skrulls show up in Manhattan.
Bendis doesn't know how to end his stories. It's rare when his ending isn't a deus ex machina.
The whole Skrull conspiracy was an interesting one that he supposedly set up way back in Disassembled or something. And he did have some interesting plays throughout, and the growing sense of paranoia wasn't bad at all except for the occasional "Bendis breakdown" (when a character written by Bendis has an inner conflict it leads to him yelling and being absolutely crazy, no matter what the conflict is).
But it seemed to me, this whole story arc was "The enemy can shapeshift to look like anyone and copy their powers." Yes, he had to handwave the whole "Why can't Wolverine detect them" issue (the answer is science!) but that was okay. The whole thing was "SECRET Invasion". The Skrulls were conquering the planet without us even realising they were there.
And it made a lot of sense. The Skrulls WOULD be an invisible controlling force. We know this because Mark Millar and Bryan Hitch already did this in The Ultimates.
So when the cliffhanger of #2 (or #3) has the Skrulls invading Manhattan in brightly coloured costumes, I lost all interest in downloading the comic because for some reason, on the cusp of victory, the Skrulls went, "RAR! NOW WE REVEAL OURSELVES SO YOU CAN BEAT US UP!" It's a SECRET invasion, remember? The only reason the Chitauri had spaceships is because they were losing an intergalactic war and had to blow up the Earth and go to another dimension. They revealed themselves on Earth because they were about to blow it up on their way OUT. Here, the Skrulls reveal themselves as they show up to take over the world. Gone is the interesting paranoia in the wake of Civil War, gone is the "Who do you trust?" element, replaced with a crappy War of the Worlds + Top Trumps = Franchise formula.
Tog, what you're saying about guerrilla warfare... What if Tony Stark discovered that the Initiative is almost nothing but Skrulls? He finds out that, oh I don't know, 90% of the Initiative's heroes are SKRULLS. And NO ONE believes him. He loses SHIELD. The one place to turn? Those New Avengers and their friends he's been hunting. The heroes go underground and have to fight the whole damn world. They don't have to just beat an alien invasion - they have to prove their IS one. The Skrulls actually show up on Earth and ask the UN if they can live on... I dunno, the Moon. Their world has been destroyed, and in exchange for the Moon they'll share technology. Because half the UN are Skrulls the motion is passed. Skrull culture starts to show up in human society (like those ads in the Marvel comics show) and so on and so on. Racism. Paranoia. Who are the heroes?
No. Big battle royales we've seen a thousand times before.