Marvel's (and more specifically Brian Michael Bendis') Secret Invasion is a comic book made in your room with your friends, talking shit while playing with action figures. The tie-ins and crossovers brought anger from the comics community, and the $3.99 price point was all most people could talk about, ignoring Yu's art and (outside of Luke Cage's semi-racist dialogue) Bendis' writing actually being good.
Secret Invasion did something most comic books don't do anymore, throwing the moral "depth" and forced politics out the window for double page spreads and issue-long fight scenes, Super Heroes saving the world from an Alien race, not sitting around talking about what to do next, or being sad asses. SI is a comic book from my childhood, continuity heavy but still entertaining. Marvel has done the unthinkable, and made two year long story arc comics popular again.
It's easy to first say to yourself "There's no way Bendis knew what he was going to do, there's no way he planned that much." You start to reread and think things like "Well Tony Stark must've been a Skrull, that's why he signed the initiative and killed Captain America." or "If so-and-so could be a Skrull, than maybe so-and-so is one too!" At first it seems foolish to be someone who falls into the "Who do you trust?" hype, but that's the best part about reading Secret Invasion, it turned readers back into True Believers.
Rarely does an "event" series actually cause a change in the comic universe's status quo, things returning to normal shortly after the books are off the new issue wall. Marvel's House Of M, Civil War and even the events that lead up to and followed World War Hulk reshaped their characters and the world they live in. The company has set themselves up, allowing new characters and series (the newly back in action Hawkeye, Nick Fury's Secret Defenders, and the War Of Kings tie-in titles) to give you a hint of what's coming, the entire Marvel Line coming together, making sense again.
What makes SI special, and I do mean special, is that it's a collaborative effort by all at Marvel, every character and book being impacted by the Invasion and Skrull reveals. Final Crisis was Grant Morrison's idea, but, even now at the end, it didn't feel complete. DC Comics didn't trust in Morrison, and added too many mini series to tagalong, ultimately confusing fans trying to keep up with everything, especially nerds (who also write great books) making Final Crisis Annotations.
It's extremely hard not to compare the two, the event books coming out around the same time, both being heavily advertised and both were to be universe-spanning. Secret Invasion has a definitive ending, it makes sense and most importantly, was an event comic. Final Crisis should have been an Else Worlds sort of thing, or something that was understood to be out of continuity. The progressive ideas Morrison may have had about where Final Crisis was going were simply bastardized by DC's barrage of mini series tie-ins that didn't really tie-in.
The major flaw of SI is that there may have been too many tie-ins that weren't new mini series, particularly with the New Avengers, Mighty Avengers and Avengers: Initiative, essentially putting your regularly scheduled programming on hold so you had to concentrate on the main event. They were too involved, and held pieces of the bigger picture, Marvel did a good job giving you bits and pieces to inform you, but it pushed you to buy more and more, a bummer at the $3.99 price point.
Outside of the straight Secret Invasion issues, I personally only read the X-Men and Inhumans mini series, not really caring about the other things going on. The new "recap" page in the front of Marvel books reminded us what was going on, and news broadcasts shown in the actual pages updated the reader on what was happening in books they may not have been reading. You never felt out of touch or detached from what was going on.
Now, with the collected issues coming out in hardcover and paperback, it's incredible to read the comics I didn't read monthly, seeing differences and figuring things out, watching the destruction of the events of Secret Invasion, which take place over the course of only two days or so. It also branches out into the Dark Reign and War of Kings separate event books, War of Kings taking place in space, reintroducing Marvel's cosmic characters, some of which I thought were lost forever.
Like most of Marvel's events, it feels like the moment it lead up to was a boner kill, the entire series ending with Norman Osborn (the Green Goblin and leader of the Thunderbolts, duh dudes) being the hero at the end of the day, which leads into the Dark Reign and the Dark Avengers.
All their books are connected, and it does mean you have to try to follow some continuity which some people can't handle, but catching up isn't hard. Everything is in trade now if you're willing to dish out the cash or you know, go to a library. With comics becoming popular, one shots and mini series are popping up everywhere, it's easy to get into any character you'd like, even dead ones like Captain America.
Continuity heavy comics are the only way the nerdy bullshit we love in super hero comics is going to survive outside of weird and kinda fun nostalgia comics like Old Man Logan. Haters of Secret Invasion just never gave it a chance, even the introductions were more captivating than whatever Superman mini series was going on. We don't want reality in our fantasy, so stop acting like you do. Y: The Last Man may be popular, look good in trade on your shelf and be acceptable to your girlfriend, but you're reading it because it's Science Fiction. Secret Invasion is so pure, it's brightly colored super heroes fighting a bad guy they all understand is bad, and winning. It's just, you know, no bullshit.