I think - like it's been said - that the game will have all the major plot points answered in the final game. This was the filler for the middle of the series to set the stage for the final confrontation. And if you get to keep at least part of your squad for ME3, then it will make sense for doing all the side quests, or even if it affects the story, whether you get to use them in the third game or not. What I'm saying is, maybe going through all the side quest hoops you did in this game also affects the outcome of the third game in that you have a larger, more loyal group that makes a much more formidable opponent when the reapers begin there assault. This is all guesswork and speculation on my part, or perhaps just wishful thinking as well.
I will agree that at certain points, it did tend to meander in the storyline, but it was filled with so many "OMFG" moments towards the end, and even throughout the game in general that were on par with the same feeling I got from God Of War 3 (though obviously for different reasons), that I felt it was worth it. And I'm sure all of the small endings and revelations (the Geth being united or the "heretics" being destroyed, Haelstrom's energy crisis, etc.) will all be tied to the final game.
As for the Collector / Prothian indoctrination, that happened long before the events of the first game, with EDI mentioning they'd undergone many generations of genetic mutations, and many of the characters and "Mass Effect Ascension" both share knowledge that the Collectors have been around for quite some time, just that they are so reclusive and advanced, that many believe they are a myth (like the mechanic in the Terminus Systems who states that he believed "they were just a story..."). I believe they were sort of a "plan B", as the Reapers become more and more desperate, with the Keepers ignoring the signal and Sovereign's destruction, Harbinger and the other Reapers have become desperate to the point of abandoning their Mass Relay invasion strategy and attempting a direct assault against the sentient beings.
So...to make a long post short, I semi-agree with you. But the game was so ridiculously good and fun and I see the merit of what they did. And it's one of my favorite games I ever played. But....more importantly, who thinks we need a Volus party member in ME3? Come on!