Highly populated market place. I would think that being different in some area would help marketability. If you aren't going to make it cheap, it has to be different. Otherwise, why bother?
So, from that standpoint I see a committed frame to either gears or single speed- no "do it all" type as we have myriads of choices in this type of steel frame. I realize it is hard from a marketing planning standpoint, since the bean counter, (who ever that is) isn't going to like you alienating a segment of the market place, but again, if it isn't different, why bother?
Internally route cables, or make cable stops that are removeable, ala Ted Wojik, so you could run full housings to gear up a single speed specific frame with an internally geared hub.
EBB's are good if you use the right one. I like the split shell EBB on my Blackbuck real well. Another cool, (and lightweight) option would be to use Niner's EBB.
Mount the rear disc caliper on the chain stay. Provide rack braze ons.
Clearance for the biggest tires on Gordo rims with mud clearance.
Here's some thoughts on some of the requested features I keep seeing.
Short chainstays: Lots of people will say they want this and a high BB. Neither has ever been historically successful in the marketplace, nor been proven to be great for all around trail riding. Sure, some specific instances will prove out those features as being "good". But you will be selling to several folks (hopefully) with a wide ranging taste in what makes a bike work- or not, from all over the nation/world. "Short" becomes relative then, and so does "High". My suggestion would be to go no shorter than 17.25" on the chainstays and no higher than 12" on the BB.
Finally, the short head tubes are not all that necessary as you get away from a medium sized frame. Large, XL, and (hopefully) an XXL frame should be able to be set up without a ton of spacers so that a 7-10 degree stem gets you at a point where the saddle to bar drop is 3 inches or so with a flat bar. I've seen some that require a stack of spacers well over an inch to two inches to accomplish this and that is nutty.
That's my two cents............