It feels like it's been forever since this show's been on my TV. I thought I was getting spoiled by the awesome storytelling of Young Justice, but then Avengers shows up and offers up an equally compelling story of their own.
First off, this was the best depiction of Doctor Doom that I've ever seen. It takes only a couple of minutes to see exactly why Doom is the single-best villain in all of comics, as he single-handedly takes down the Avengers and the Fantastic Four one-by-one without breaking a sweat and then lets them go, simply because the outcome doesn't matter since his plan was pretty much dead on arrival.
Speaking of which, the subtle movement on the Secret Invasion front was superb! The seemingly-inconsequential quotes like Doom's "You do not even see what is happening here" to Reed's even more subtle "Sue seems to be the one ignoring ME these days" make the reveal at the end of the episode that much more mind-blowing.
Also loved the callbacks to the comics, namely the Marvel poker nights and the rivalry between Hulk and The Thing.
I also thought it was funny that Skrull Cap's asking about Johnny Storm was taken as a joke; with Hawkeye seeming to be impressed with Cap developing a sense of humor. It's little moments like this that show impressive character depth that isn't always found in cartoons.
I think it's because Faraday's theory -- that you can't change the past -- isn't correct, or at least doesn't apply when Desmond's concerned. So Desmond didn't actually have that memory until Faraday changed the past. Or something!