There are many reasons a manuscript can be rejected. When an agent or publisher rejects your manuscript, they will give you feedback on why they think your work is not good enough for publishing. When you receive this feedback, you have a couple of options. You can heed their advice and make the necessary changes or, if you believe in your story, you can choose to stick with it because it is possible that your story is actually good enough but it just was not right for that particular agent or publisher.

However, there is a third and often more practical option which is to go through the feedback, decide where you feel the feedback is fair, and revise your manuscript accordingly while leaving intact the parts you feel do not need to be changed.

What To Revise:           

The Subplot Is Taking Over The Story: Subplots are very important in any story and they must be used to add more details and help the reader understand the characters better. They are especially helpful in character development. However, they should only be used to complement the main storyline and not to compete with it. If you find that any subplot is starting to take attention away from the main storyline, you must scale it back. So if your agent advises that a certain subplot is taking over the story, please heed their advice and revise the novel accordingly so there is no distraction from the main story.

Conflict Not Strong Enough: Conflict and the desire to see it resolved are what drive a story. Your reader will be looking forward to getting a resolution and hence closure to whatever conflict formed the pivotal focus of the story. This conflict needs to be solid enough to grab the reader's attention, so if your agent says that it is not strong enough, please revise it.

Confusing Structure: One thing that your narration must have is seamless flow otherwise the story will be lost in the confusion. This is often very common with multiple POV novels - stay away from these as a new writer. It can also happen in single POV novels. Your novel should have a predictable structure that your readers can easily follow. Structure here refers to many things including POV, chapter length, flow of events etc, but it does not refer to the plot itself so do not make your plot predictable but rather the structure of your novel.

What To Ignore:

I Was Unable To Connect With The Voice: The voice of your novel comes from your personal writing style and not everyone will be able to connect with it. Your voice is your voice and it is therefore not something you just sit down and change. This comment simply means that was the wrong person for your novel, so ignore it and just move forward.

Character Is Not Likeable: Your characters, depending on the roles they play, do not necessarily have to be likeable. They simply have to be believable. Character likeability works just like in normal life - it is very subjective. Different people will like different characters so pay no heed here.