A few excerpts from Janet Reid, a literary agent:
Good premise, but the rest of the novel didn't hold up: 11Her complete list is here. Out of the 124 full manuscripts she requested to see, she signed only two.
Not compelling or vivid, or focused; no plot/tension: 10
Slow start or the pace was too slow: 9
Structural problems with the novel: 8
Interesting premise, but not a fresh or new take on familiar plots/tropes: 7
Had caricatures rather than characters: 2
Needed more polish and editorial input than I wanted to do: 2
Good books but I couldn't figure out where to sell them: 7
The editor's list was also compelling. It revealed that sometimes your manuscript may be rejected simply because it is not what the editor was looking for.
An excerpt from the list by Del Rey editor, Betsy Mitchell:
Not what Del Rey is looking for (meaning we had enough on our list already of whatever subgenre was on offer): 22
A good manuscript but not right for our list (included a couple of nonfiction SF-related titles more suitable for a small press, the odd children's book, etc.) 14
Not a genre that's doing well right now (horror, mostly; some foreign novels being offered for translation, anthologies whose concepts weren't strong enough) 18
It is sometimes very hard to understand why the manuscript you love so much isn't picked up by an agent. The list above is a good starting point to make sure that any manuscript submitted is the best it can be.
The editor's list is probably a lot more eye opening to a lot of people. There is a belief that if a manuscript doesn't sell there is something wrong with the book. That isn't necessarily true. My own agent says she gets a lot of manuscripts sent to her that are good stories, but nothing makes them stand out. She has to reject them because she knows she can't sell them. Therefore, you may have an awesome manuscript on your hands, but it just might not suit the needs of the publishing houses. It may take a lot of submissions by your agent to finally find the right fit.
As my agent told me over and over again, "It only takes one."