I take mine out of the box, put them on the track, and run them as is. It has nothing to do with resale value (I've never bought a toy, whether it's $5 or $5k worrying about future value). I run the crud out of my trains, repair as necessary, meaning replace worn traction tire, etc.
I am not really a modeller, per se. I'm still the kid who just likes to play with trains like I did on Christmas morning 45 years ago.
That being said, I have added TMCC and new motors to my worn out and original PW diesels that my dad bought in the early 60's for our Holiday layouts.
I guess the biggest reason for keeping new trains as they come out of the big picture, I'm not really a train buff. I'm a toy train buff. I buy TMCC/Legacy and DCS stuff not because of scale fidelity, but because of the gadget factor. I'm a techno-geek and my trains are very interactive toys for me.