The pace drags during that dreaded middle section. You've heard before that your first pages need to jump right into the action. That isn't an excuse to delve into backstory or extensive narrative after the first chapter. Weave backgrounds into the story carefully, keeping the pace moving right along. Infodumps aren't effective in the first chapter, but nor are they effective in the second or third. Introduce new dilemmas if the middle chapters seem to lag, just be sure to tie them up at the end.
The story falls apart. Be diligent in looking for plot holes and beware the rushed, poorly resolved ending. Tie up your loose ends, and have good reason for them to resolve the way they do. Make sure clues are dropped throughout the story, rather than suddenly revealing an unlikely villain or reason in the last pages. Dues ex machina, anyone?
There's no character development. If you character seems perfect from the beginning, the reader's waiting for you to throw troubles in her way or reveal some secret she's been covering up with that that facade. Perfect characters are boring and unrealistic, so develop them fully and allow them to change over the course of the novel. Conversely, problem-ridden characters can make for an interesting read. Be careful they aren't unlikable, however. In order to connect with a character, the reader needs to sympathize with the MC's dilemmas. Just as no one is perfect, nor is anyone completely bad or without reason for their actions.
It's not . . . actually about that. Be sure your query addresses the main plot of the story. It's frustrating to read an action-packed query with a unique (supposed) plot, only to discover that the real story is the love triangle (and not universe exploration, after all) or that the narrative addresses the MC's brother more than it does the (dull) MC.
Checked those things off your list? Send that query, then. :)