Update: in this post, I forget that Collectors are Protheans warped by the Reapers; an important and interesting plot point. I'll leave my post unedited, and let you decide whether my complaint about the Collectors is still valid. Many thanks to CalKi for pointing out my error!
While on the topic of story, I wanted to bring up some thoughts about the Collectors as a primary enemy. The early premise of an advanced species on the edge of known space, so rarely sighted as to be considered myth is really intriguing, but I have two complaints about the Collectors: (1) an advanced, mysterious enemy is only frightening for as long as it maintains this mystique, at which point (2) an enemy needs to get personal to stay interesting, which is hard to pull from an insect.
A personal enemy was even more important in ME2 because I already defeated a Reaper. Unfortunately, the Collectors were chosen to fill the bill. Yes, they showed me a Collector General that took control of enemies on the battlefield, and yes, the Collectors stole my crew, but because I never met this character face-to-face or more importantly, believed it had a motive more interesting than an insect's, it was like trying to get angry at a hurricane for blowing things over. I can only get so angry at a bug for doing bug things.
I find it interesting that in my last post I complained about the Reapers, and in this post describe Saren as an interesting diversion that make them work. Perhaps my previous complaint was just an ME2 problem caused by the absence of a personal enemy. So what might be an alternative?
Let me throw out some personal preferences to guide things. First, I liked the Illusive Man but hated being under his thumb and having my past achievements rendered null by being blown up. Second, I wish the Reapers seemed more scarily active, rather than waiting to be rebuilt. Third, I really liked the "Legion" character and plot points. Finally, I liked where ME1 ended.
This scenario might unravel for a host of reasons familiar to those closer to the Mass Effect universe. Regardless, it's a fun exercise to try reestablishing the Reapers as an advanced and mysterious threat (e.g., by manipulating humanity) while offering up a personality to get under your skin (e.g., initially through the Illusive Man, and then Udina, who works to unravel everything you worked for in the previous game; the progress of humanity, your status as a peace keeper, and the safety of the universe). I'd prefer that over a mindless bug, especially given the franchise's emphasis on choice through dialogue.