A pimped car is always better than a stock car. But it depends on how much money you have, what you want to use the money for and if you want to 'ruin' the car or not.
Consider all these factors and you got your answer
It depends on which way YOU would garner more enjoyment from. But by painting them, they're no longer "stock" in the collector's sense of the word, and since they're both premiums, it's easy enough to re-buy and repaint, or even buy another and see how you like it souped up.
Personally, I like having one pure stock version of a car, then I do the paint job on the modded version.
I do what racer39658 does. If you're worried you can always just do the "bolt-on" upgrades instead of the permanent ones. (no weight reduction, no engine tuning)