I would agree that this system encourages the player to keep and collect cars if the cars I buy wouldn't have lifelike price tags to begin with.
Okay, a lot of race cars have a fantasy price tag because you could hardly give them a representative real world value. But otherwise, cars pretty much cost what they would cost you in real life, adapted to the credit system in GT5 of course. Used cars are used, so they cost less. All well and good, but then I can't sell the cars for a price which is equivalent to the amount of usage - how does that make sense?
Another case of "We know what's good for you, you don't!" case at PD if you ask me. If they want me to collect cars in the game, they should make collecting cars attractive to me and not punish me for not collecting cars.
EDIT:
Here's some food for thought. Why don't they make a "suggestion ticker" at the bottom of the main screen which proposes ideas what to do in the game depending on your current status? Say you've completed all A-Spec events in the game, the game could propose completing B-Spec, golding the licenses or the special events.
Getting back to the topic at hand, given you have collected all the cars you need to have for some race/challenge in the game, the ticker could suggest something along the lines of ...
You have collected all the cars you need to complete Gran Turismo 5. But there are a lot of great cars still to be discovered by you. When you buy the 1.000th car, you will be awarded the <whatever> trophy, which includes <whatever amount> of extra credits. From now on, you will see little numbers with each car in the dealerships. These numbers indicate how many of the particular models you already own. Also, a little number with a trophy next to it at the bottom right of your screen will show you how many cars you are short from obtaining the <whatever> trophy.
Very basic marketing. Suggest what the player could do, tell him what bonuses await him to demonstrate why he should do it, support him doing it.