I think creativity is stimulated by constraints. A blank canvas can be terrifying to an artist. Consequently, one can save a lot of time by focusing on designing a control scheme that is both ergonomic and articulate. It is a mistake to provide the player with an interface which is clumsy. Players want to express themselves, to feel empowered not disabled. It is always possible to rebalance the puzzles / obstacles / enemies later so that they don't find it lacking in challenge. Story and characterisation is good for marketing purposes (as a 'you get to be this guy' silhouette is about all you can use for the box-art, as you can't convey what it feels like to explore the dynamics of the game's rules), but you ought to shelve all of that until you have settled on a control scheme that puts the most frequently used actions in the most convenient to access locations (i.e. the majority of the game can be played via a gamepad without moving your thumbs off sticks).
I use a program called FoldingText for OS X to group my notes beneath collapsible headings, but I expect a Wiki would be okay too although I wouldn't know how it would allow you to get a sense of how big your project had become as it would be hiding everything behind links. Really, as soon as you can you should get a prototype working with a feedback loop in it in order to judge the feel of the controls and decide upon where to place and move the camera. This should be done before any real work on its aesthetics - Super Mario 64 started off as an ball with inertia and during development they made the mistake of having him turn faster and Miyamoto picked up on the fact that the game seemed "boring", identifying it was a lack of drama (i.e. reversing direction at the last moment when near the edge of a platform being much more exciting when the turn around was as sluggish as it had started out), they fixed the relevant parameters and it resulted in one of the best games of all time.
> For markdown hiding, we are still searching a good UI/UX solution.
Have you tried FoldingText? It hides all Markdown until the cursor is over the affected text. I think it's a lot more elegant than an edit/preview model since for most people reading and editing are continuous and intertwined.
I have FT, and while I don't use it regularly, I have kept up with with it through its long revision process. If you search around you can find plenty of reviews that will give you a better overview of its features and so on than I can here.
But, as for my personal opinion of the app, I think that at its current discounted price the app is worth the cost if you specifically need an outliner/planning app. I think that the biggest problem with FT is that if fits a weird niche: true, the interface is easy-ish to use, and offers quite a few nice amenities (e.g., focusing, quick navigation), but I don't know that these features alone make it worth the original price. The 'power' features it includes—scripting, plugins, and all that—are interesting, and others may find those more useful than I do, but I suspect that most people who will be interested in the deep features will already be using effective, powerful alternatives. This is certainly the case for me, as I use Vim + plugins (Vimwiki, Notes) to replicate much of FT's basic feature-set, and nValt (or Notational Velocity) to cover the basic note-taking aspect. While I like the nice interface of FT, for me it doesn't offset the annoyance of needing to load up a dedicated app every time I want to outline something, especially when I can use Vim for all of my plaintext projects. Ultimately, I think it is an interesting idea that is nicely implemented, but every time I try to do something with it I find that my other (free!) tools do the job with less fuss.
But, YMMV, and you might try downloading the trial version just to see how the app works: http://www.foldingtext.com