Some functional, some cosmetic
One of my pet peeves when talking about customization options is when product purveyors list the total number of combinations as if it's meant to be impressive, because it doesn't actually take very many set elements to produce astronomically high numbers of combinations. A more useful metric is simply how many elements exist; that is where Grand Theft Auto V impresses.
In a brief interview with Game Informer, GTAV mission designer Imran Sarwar discusses customization options, including both weapons and vehicles, but focusing on the latter. The upcoming open world juggernaut will boast over 1,000 different pieces of custom vehicle parts. These will range from functional components like brakes or armor plating to purely cosmetic things like window tinting or paint jobs.
It doesn't sound like the system allows complete freedom a la ModNation Racers, but with social functionality in place, it seems like Rockstar does want you to be able to make a car or bike your own, and then share your creation with the world.
Grand Theft Auto V Q&A: Customization [Game Informer]