I proposed exactly the same in October with further elaboration, so I agree with you. Full description here:
Well, your question is valid because it discuss actual design-decision and its influence at actual gameplay.
First, I like the overall Item system, Paint included. I also understand how many players are annoyed by it, because they feel and find it as unnecessary complication. However, that system is pretty unique from many standpoints, not just actual execution.
From my perspective, initial foundation of the Paint Chip system lays in one of the unique aspect of Gran Turismo series where all cars have "real-life" paints/coating for every model. From the very first 1997 game all dealership-cars are painted into their original paints, named with proper manufacturer-names and GT series is really unique because of that. Development of the "GT Auto" feature introduced a Paint Shop as a part of the overall ownership/maintenance philosophy of the GT series and Paint Chips are created as a tool for the usability of the Paint Shop.
Second, creating a live and vibrant "community" was obviously one of the main focuses while designing community-goals of GT5. From the very functionality of user "Lounge", over options for "sharing" things (B-Spec drivers for Remote Races, Cars over Profile functionality), all the way to "Gift" option that allows gifting of all items in the game that corresponds to the "Item" category (driving gear, tuning parts, car tickets, actual cars, horns and - paint chips).
Third part of my rationalization is existence of the Used Car/Online Collector car dealerships.
I presume how Polyphony's intention was to create a "game inside the game" aimed at the community and Friends in primary-focus, where players would be given Paint Chips as a bonus for buying the car in color they like (at least for the majority of cars). Obtaining a Paint Chip allows a player to either paint a desired Used Car to color he wants, use that color on new Dealership car that does not come with his preferred-color or to gift it to his friend who is fond of particular color/manufacturer.
Also, Special Polyphony Digital Paint items (chrome/matte) were obviously created as a way to additionally award players for their progress in Collector-aspect of the game and to create a Special Items that are awarding some accomplishment.
*Problem* that many players have is - at lest I presume that way - because all other games in the genre went easier way and just allowed for a car-painting as a given, fee of hassle and free of charge.
Another *problem* is how introduction of the game-backup functionality - which was needed - allowed for development of the "dupe-community" where "trading" became more important than "gifting" (worth noticing is how same happend to car trading, gear trading, etc.).
Personally, I like the Paint Chip system and I really have no problem with it whatsoever. I love white cars with black rims and during last 12 months of play I really had no problem whatsoever to paint all my cars in different shades of white. Besides having great amount of Paint Chips from my original Dealership-purchases, many of my game-friends were gifting me white-chips and I was gifting them their color of choice. No duping, trading or exploiting a system was needed. Further, I really enjoy in that small "game inside the game" aspect and have been painting Used Cars into original manufacturers colors from the very beginning. All my used Nissans are painted into shades of Nissan's whites, Mercedes at Mercedes ones, etc.
However, I can also understand how many players find that system as complication and I also think how PD could have solve it - together with the recent problem of getting just one Paint Chip per color in DLC (which I also do not find logical) - with introduction of the real Paint Shop.
In my view, real Paint Shop would allow players to choose the manufacturer and the color (Paint Chip) they like in quantities they want and purchase it with their in-game Credits as a regular "Item". Also, Paint Shop would also offer an option to "Buy" paint-chips from players by discounted price (as an "used item").
In addition, you could only buy colors from manufacturers whose cars you have in your Garage. New manufacturers would "unlock" with obtaining their models
Of course, further functionality would lock ability to buy any "Special Color Item" (matte, chrome or special) as long as you do not actually obtain it in the game (by reaching some goal or buying DLC) which would than unlock it for purchase at "Polyphony Digital Paints". In addition, we already witnessed how "gifting" (trading) ability can be restricted per-tem-basis (DLC paints are non-tradable and non-dupable) so there is an option to preserve "specialty" of the Special Paint Chips even with such Paint Shop system.
That system would preserve original aspects of ownership/maintenance philosophy of the GT series, would expand GT Auto functionality, would allow players to sell colors they do not like or do not want to have back for Credits and would give further initiative in actual gameplay (gain Credits to buy *something*).
Same logic of Shop could also be imposed for non-special Driving Gear items, etc.
Overall, I love the Paint Chip logic from gameplay-design perspective, but I also think how expanding it in form of Paint Shop would benefit for perspective and usability of both gameplay and players.