Well this is awkward, one of us is gonna have to change XD I, too, have a place in my current project called Caligo, haha.
I think you have an interesting premise here! I found the plot easy to follow, but I agree on the points you listed above--the pacing is very fast, the characters aren't given a lot of depth and development, and if it plays out exactly as it's written right this moment, it will be a very short game indeed. But that's not a bad thing! The thing about first drafts is they're never polished. That's why they're first drafts.
I don't think that having some dialogue early in your workflow is necessarily a bad thing--but in terms of painting out the broad strokes of what's going to happen, it can sometimes bog you down in the details. (Says me, the master of being bogged down by details.) My design document has some of both, but it's mostly bullet points.
I think that as you add in side quests, it'll help flesh out the characters and bring in that depth that you want. Likewise, as you start giving depth to the characters, side quest ideas will start to pop up. You don't have to write down every line of dialogue as you do this--like gstv87 and KazukiT said, bullet points and descriptions are fine. That, in turn, will slow the pacing of the plot a little bit, while also helping to build up the world.
For example, you can have NPCs remark on some of the other, specific things Simon has done. You don't have to chronicle every detail of how he developed a public transit system (for example) but having an NPC mention that it took, say, 14 years to complete because people kept trying to stop it would demonstrate that he's tenacious. You could have NPCs mention the way adventurers used to come to burn and pillage, and how great it is that that isn't happening anymore.
And Whitly, you could do a lot to build up his character as well. Someone could mention a previous assassination attempt that he foiled, or that he was instrumental in getting the emergency rescue services up and running, that sort of thing. It'll be a little bit harder of a punch in the feelings when the player kills him for real.
Also, getting that wooden stake could be a semi-side quest. One of those things that sounds like a sidequest, but turns out to be main story--though you'd have to frame it in such a way that it's unmissable without it being immediately obvious that you're going to try to stab a vampire later.
Five is an interesting loose end. If I was Mist, I'd be snapping mad with him. I think there's an opportunity there to fit a little more plot before Mist heads home, if you so desired. Or Simon would have some more work to do, convincing her to drop it.
And I like your sense of humor! Mist's exasperation with this very tidy "dark" world, the joys of travel like lines and customs, and I got a particular kick out of "Henry Mason and the Turnabout MacGuffin."