the champion is champion for a reason - they have the most points.
regardless of any other driver having exceptionally good races, the one who has the most points at the end was either the most consistent, or got the best they could over the course of the season to end up with the most. its simple. they might not win every race, they might not win any, but if they won the championship by strings of second places, okay its not as nourishing as a race win in first place, but it would mean consecutive consistency where others either failed or didnt do as well as the consistent one.
in todays age, engine and mechanical failures aren't as commonplace as they use to be. this could suggest that perhaps todays 2000's generation of driver is less likely to lose points by mechanical fault, and more so by a driver error. meaning, the champion is going to be the highest scorer on regular good driving - but if, ie Massa or Hamilton make a lot of spins and dodgy racing moves that lose both of them points, and then someone like Kubica ends up with the most points - the others may have had more wins, granted, but Kubica has been there where the others have failed to perform - most of which, being the 2000's, points lost for lower quality driving and not engine faults.
it seems today, the WDC is going to be someone who makes the most of what they can on the day, instead of the nitty gritty racing for the win of the 90's and before. perhaps the reason is because in the days of senna and prost and the 86 turbo days, you didn't know if your engine would go bust that race or the next, so every point was precious. that made the racing more aggressive, and with only the top 6 getting them, even more so.
today you can cruise from third to first and the need to win is less, largely to the points. (and maybe now added to this the penalising for making an overtaking move!?).
so all in all, consider this:
what if a driver has a one-off win and never scores all season (ie, Piquet), earning 12 points, versus another driver who regularly finishes the last races with 2 points per race (ie, Vettel). they both have the same points, so which would be conceived better of the two? mr one off performance, or mr consistent?
the old system would naturally place piquet higher per wins in the standings next to eachother. so i guess that way wins is the main factor.
but really, in my opinion, a solid finisher is more worthy in this case.
of course, if someone won more, they would by default have a lot more points than someone in second every race, so naturally the winner is clear.
but this year is unusual - and its a personal argument what is more deserving.
for me, i would LOVE to see kubica take it for his consistency, but it is hamiltons win at silverstone and other races ie, spa, that highlights me as more deserving than kubica, and by the fia way, hamilton would win it if they were to get equal points.
so there we have it - wins are what counts as the fia process it all at the end.
Jenson drives it like he owns it; Lewis drives it like he stole it