So gentleman a question. I own a 09 Honda civic lx-s sedan 5 speed manual. I was considering keeping it when the FT-86 gets here, but now I am pondering trading the civic in for a prius and still purchasing the FT-86. What do you guys think? Prius or keep the CiviC?

What does "age well" mean to you?  Do you mean that in a few years the next purchaser will pay extra for it?

Then nothing.  Nothing you will do to this car will hold up resale value unless you keep it absolutely bone stock and dont drive it.  Then in thirty years, if there is still gasoline, someone may be hot for it and it will hold its value.



If by "age well" you mean you will still like it in a few years and not be sorry to spent the money, then that is far more personal.
 
For me, that would be good wheels, good suspensions, maybe FI. 

I dont think those would add anything to the resale value of the car.