The perfect example of a car that isn't half a century old that holds value very well is the "last of the air cooled" 911 cars (993). A well taken care of 993 Turbo or even 993 Carrera S Widebody carries a serious premium these days. 40k-85k for a car from the mid-late 90's.
The only M3 that has ever appreciated in value significantly is the E30. The E36 has no chance and neither does a non CSL E46 IMO. (I know I am leaving out examples like the E36 LTW and E46 GTR etc because they are much rarer).
I think that the E9x will depreciate as any modern M car has. Don't ever see them actually going up in value unless you store one in a chamber for the next 70 years and go sell it at auction when you're 90 years old or dead. I reckon that the E9x will be remembered fondly as a very nice car, yet it probably won't be as desired in 16 years as the 993 is today. It's too cheap of a car to begin with for enough people to keep them in good working order to support any kind of a solid second hand market far in the future.
I also think that in the future...I mean 10+ years, the E9x will be more desired in 6MT. This tech simply does not advance or age at this point whereas I predict DCT will become a complete relic. Especially the way things are going, it will be harder to find any manual transmission sports car, let alone a gas guzzling high revving 8 cylinder.