The main character starts the process. I'm looking at their development - is it logical? Do they make any sudden jumps that are inconsistent? Have I explained where they're coming from? Do they have enough conflicts? Should I add another level of difficulty to their lives? They carry the story, so they need to be strong enough. If not, they need extra scenes to show how and why they're changing or behaving in the way they do.
I expect my main character will be present in all of the scenes as I usually write from a single viewpoint, but if I was writing from a multiple viewpoints I'd be checking that everyone their fair share of the story-telling. When I did this process with Adultery for Beginners, I discovered that one character dominated the story telling. I decided they deserved to take centre stage entirely and took out the other characters' viewpoints. This involved a serious rewrite - I eventually changed about 90% of the scenes. Painful, but necessary.
But even though I write from a single viewpoint, I want to make sure that the secondary characters have their own story. I don't want them to be just hanging around for the main character to show up, they need their own lives. For example, Lorna in Kissing Mr Wrong changed to Briony in the subsequent drafts and got a life. She goes through her own development and her own story and her life has changed by the end of the novel. As a writer who is a former actor, I like to think that there aren't any duff roles in my books.
I'm also looking for gaps. In Nice Girls Do for example Anna goes up to London to stay with her boyfriend Oliver, who she's completely besotted by, and everything else gets left behind including the lovely Will who isn't mentioned for pages on end. Now it's reasonable for Anna not to think about Will as she throws herself into Oliver's luxurious lifestyle, but I didn't want the reader to forget him. So I had to add a couple of quick scenes to keep Will, if not physically around, then present in Anna and the reader's consciousness. You'd do the same thing if, for example, you had two main story lines but one of them was on the back-burner for a while.
By now the index cards are getting a bit messy. If I remember I use one colour initially, then use a different colour for added scenes. I staple scenes together if I'm going to combine them, make lots of notes, rewrite the card if it's getting v untidy. Finally I've got a stack of index cards that I'm happy with. At this point I re-write the novel from start to finish using the cards to guide me. When I started writing novels I needed to do this process several times. When I'm happy with the shape it's on to the next stage.