Okay, I think I'm the contrary one here.
I have Founder's #19 (second owner), and (to my wife's anguish) I have not worried about keeping it original or worried about devaluing it. Mine is not meant to be a collector's piece, it's my car to enjoy and have fun with for as long as I have it (which will be until my 2020 Roadster arrives). Before I'd had it a month, I got the dash changed out to allow for a double DIN stereo, because I love music and there was no way I could read a postage stamp sized GPS display.
The paint job was four years old and a bit rough by the time I got the car in 2013. It was Signature Green, which is very dark and shows all scratches and swirl marks vividly, plus I really wasn't all that fond of the color. So a couple years later I had it repainted and have no regrets whatsoever. I had it done at a high end paint shop where they spend most of their time doing quality paint jobs for collector cars that only leave the garage to be in a car show. And yes, it was definitely pricey, higher than any of the numbers that were mentioned in above posts.
I had it repainted Lightning Green and it gave the car a completely different personality and really made it feel more like it was mine (since I wasn't the original owner). My wife was actually happy with it since she says it makes my tiny car more visible in traffic so other people won't hit me.
Only two drawbacks from having it painted: 1) The tan interior didn't really go with the new car color, so I ended up spending more to have the seats and door panels reupholstered with a bright green marine grade faux leather. 2) I had never really contemplated the carbon fiber accent pieces when the car was so dark, but once it was a bright color, those accents would really pop, so I ended up spending another chunk on those.
So my advice is that if you are going to own a car as much fun as a Roadster, go ahead and enjoy it as much as you can and don't worry about what will become of it when you're finished with it. Maybe it will change the resale value, maybe not. But specifically on the paint job, if you can find the color you want to begin with, you will be far better off, because it definitely isn't cheap to change it later.