While I wouldn't call the ME timeline and story thus far a "complete mess", I will say that ME2's lack of true direction is the cause of most plotholes.
In ME1, we were given a very clear threat: the Reapers. We knew there was going to be a sequel, and we knew it was going to be about stopping the Reapers when they inevitably attack our beloved galaxy. It was simply a question of how, when, and eventually, if we were lucky, why.
Enter ME2: What was its purpose? The Reapers still aren't here. But the Collectors are. Who are the Collectors? They're bad people abducting tons of humans. Why? Because... er... Reapers!
So we save what humans we can, destroy the Human Reaper before it's even close to complete, and kill the Collectors. Awesome.
But where does that leave us?
...Right where ME1 left us. The Reapers are coming, and until Arrival, we still don't know when or how. We just know they're coming and we'll have to fight them in the sequel.
So when looking at it that way, what was the POINT in the Collectors attracting the attention of the galaxy by abducting hundreds of thousands of humans? Couldn't they just wait a bit? Couldn't the Reapers have come (Arrival) during Shepard's hunt for the Collectors, thus distracting whatever human threat while they took the back door straight to Earth?
ME2 offered a lot of character interaction, a huge elaboration on Cerberus and what happened to the Protheans, and succeeded in at least advancing the timeline. Other than that... It pretty much didn't change anything. If ME2 didn't exist, and ME3 was ME2, what would change?
There wouldn't have been Collectors, Shepard wouldn't have "died", we'd have less companions to be pals with, and Shepard wouldn't be as intimate with Cerberus. Other than that, nothing. We wouldn't be missing anything; we'd be at the point in which the Reapers come, and we fight them.
Yes, there are lots of smaller scale subplots at play, such as Omega's status as the pinnacle of the Terminus, the Batarians on the verge of war with Earth, the ever growing problems on Tuchanka and Illium, etc. But in the grand plot? ME2 advanced virtually nothing. Hence all the gaps in the story-- they aren't necessarily "plot holes", but rather, gaps that aren't really filled, and we aren't sure why they even exist. Do we need to know why the Reapers wanted a human version of themselves? Do we need to know why the Collectors even existed? Is Shepard's "death" going to influence anything whatsoever?
We'll find answers, I'm sure. But none of them are essential. The overall threat remains unchanged whether or not we have that knowledge. "We fight or we die, that's the plan." As ridiculous as that quote is, it actually sums up the gaps in ME2 pretty well. We're left with, "Who the **** cares? They're REAPERS! Kill them or we die!"
[/rant]