I really hope not; if this happens it will mean a lot of people will never win the cars you get as a reward for completing a racing series; which would alienate a lot of the casual GT players. I know a lot of people that have played through the series, winning what races they want to (a lot of them don't do the 24 hr races for example) and getting the prize cars from them. Some of them don't even bother to BUY a car in GT, they use the ones they win, end of. If Kaz and the team go down the road of "if you win this online championship, we'll give you this Bentley Speed 8 LM race car", how many people are going to A) achieve that (as there are some seriously quick racers out there, and B) lose interest oh-so quickly because they've been punted off for the 5th time today? Lets not forget any kind of 'online-only' GT will have to be on public servers, which has not proven to be brilliant so far, lets be honest.
I like the GT series for its huge single player challenge, I like being able to collect, tune up and race every car in the games, and now, with Prologue, I like to be able to go online occasionally to see how I stack up. Taking one or the other away from the series now would be derogatory IMHO.
Now that I think about it, how would a championship series work anyway? you would have to race against the same people for the entire thing, and thats just not going to happen in the Polyphony Digital cup at 10races x20 laps each or whatever it will be.
Of course, if PD decide they want to do special 'one of a kind' tournaments where the winner gets a car no-one else will own, then ok, I guess I can get on board with it, as long as its something totally random as opposed to an Enzo or suchlike. A lot of us on here play GT as we get to race cars we will never, ever own in real life; making those cars online tournament winner-only cars will take take that away from us and leave us racing Honda Civics, which for me would ruin GT's magic.
mini rant over