Montezemolo may say that the record books will show Felipe won more races, and he's right, the blinkered fool neglects to mention that the record books will also show Hamilton as having scored more points.
Regardless of the points system it has always been, and will always be, that the guy with the most points wins it. (Yes I know about 1988 - Effectivly though, Senna - after selecting the best results - had more points)
Personally I like the new system, I always thought 10-6-4-3-2-1 was a bit too biased towards race wins, wins aren't everything. In football you don't win a league just by winning some games, you have to perform consistently, in tennis or golf you don't become ranked number one by getting a couple of HUGE wins, you do it through consistently finishing well.
A sport that encouraces nothing more than flashes of brilliace isn't really a sport in my eyes. The guys still want wins (it gives more points) but whats the point in driving like crazy for 4points insted of 2 if when doing so your engine turns into a hand grenade?
In 1981 Keke Rosberg won the championship having scored only ONE win...it was consistency that won the day (even with a system that is biased towards race wins). In 1992 Nigel Mansell won it having won 9 races on the trot.
The point is, either way you want, you have to be consistent. Race wins are not, and probably will not be everything, unless the points are more like 20-10-8-6-4-3-2-1, but that would ruin the sport because lower points positions would be rendered inadequate, so nobody would give a damn.
Personally I think the 10-8-6-5-4-3-2-1 system is brillaint, yes you can argue that Felipe might have won if it was the old system, but its not the old system, and thay all have the same rules to play with, so its not unfair to anybody. If Felipe was good enough this year to win it he would have, he missed JUST. And thats a pity. Even if the old system was used, who to say that Mclaren & Ferrari (and the rest) would have run the same race strategies? It COULD be that had the old system been used we'd have had exactly the same result.
To look at results which have been determined by running to 2008 sepc rules, then say NOW WITH HINDSIGHT lets apply 1998 spec rules is silly, as if those old rules had been used the season would not have panned out the same way on track, some would have been more agressive in quali, or the race and soome may have been less agressive so as not to fall from the lead of the race.
I like the 10-8-6-5-4-3-2-1 system we have now because it means that a string of wins in the mid season does not mean you get the title, you have to fight to the end. Who wants a title wrapped up by July? Nobody (except the driver who wraps it up by July of course lol!)
Old system or new, the man who performs the best within that set of rules will always win. What if's mean nothing, "What if they were allowed Turbo's" well they're not so who cares? lol...my point is, is that Formula One is exactly that, a set of rules that make it F1, the F1 world champion is the champion of F1, not the champion of Le Mans, or ALMS, or ChampCar, or IRL, or F3.
If the rules were different It would still be F1, just a slightly different F1, in which case maybe a different driver would win, but then again maybe not.
eg. In 1988 Senna won, we had turbos, he drove turbo cars well. In 1989 we didn't have turbos, he still won.
In short, the guy who plays the game best always wins. If the game merits consistency, the most consistent win, if it merits win, the one with the most victories wins. But the guy who plays it best, always wins.
EDIT:
P.S: Sorry it took so long!

Silence is golden when you don't know a good answer.