Lots of points contribute to why they are expensive. Small scale production is one of the main reasons. For example i know that if Chumba were to increase their production run by 4 times the cost of the frames would reduce the cost and sales price by a very good amount, but they simply don't sell enough to warrant the extra volume.
R&D is expensive, but it doesn't have to be prohibitively so, especially for the small companies who can do small prototype stuff from a work shop (as Chumba do).
Of course there is also supply and demand, everyone wants an Orange 5, Lapierre, other flavour of the month bikes, thats why they hold their value well in the shops, not many sticker discounts to be had keeps the prices in check and demand high, couple that with small runs of production and it contributes to expensive full suspension bikes and frames.