Since you say its not fair to look at the season as two halves, lets look at some statistics from 2006 :
So were Red Bull in 2009. In the hunt for podiums, if not wins, from the outset. Button was nevertheless one of the most consistent drivers of the season. Point being that if you have such as massive advantage in terms of the whole package (car + tyre + reliability + balance + starts) you wouldn't need to push as hard. Cruise and collect drivers will always be more consistent while those that're driving cars off the pace will naturally need to push harder = more mistakes. Renault basically picked up from where they'd left off in 2005, while Ferrari were off the back of a dismal campaign in 05 and were still getting to grips with the Bridgestone issues, which still plagued them in 2006: remember San Marino?
There's way too many factors involved to categorize the season neatly into two halves. Performance was both circuit and tyre dependent, it was not as simple as the fairy tale stories that are usually presented on here make it out to be.
Ferrari vs Renault :
Wins : 9 vs 8
Podiums : 10 vs 11
Top 4 finishes : 24 vs 19
Pole positions : 7 vs 7
Top 2 qualifying : 16 vs 11 (would've been 17 vs 11 since Schumacher was good enough for atleast second place)
Top 3 qualifying : 20 vs 15 (again, should actually be 21 for Ferrari considering Monaco)
Reliability related DNFs : 1 (Japan) vs 3 (Hungary, Italy for FA and Bahrain for Fisichella)
I can see that Ferrari have more wins, equal number of pole positions, almost the same number of podiums, more front row qualifying, more top 3 qualifying, less Reliability related DNFs and more top 4 finishes than Renault. From this we can actually conclude that the Ferrari was marginally better, however their qualifying issues in 2 races would mean its reasonable to peg the two teams as equal.
I dont see how you can make an outrageous claim of Renault having the 'massively better package' when every bit of information points to the contrary.
Here's where the difference lies between the two teams for 2006 and the reason why one team won both championships while the other went away empty handed :
DNFs due to driver error : 4 vs 1 (2 each for MS and FM and 1 for GF)
The Mass Dampner was on the car since 2005 IIRC. It was approved by the FIA and later banned because they later decided that it was a moveable aero device (which made it similar in function to Ferrari's flexi wings).
The flexi-wing issue was outside Michael's control, too. I don't think the penalty was justified, at the time I laughed out loud when the question of Felipe having been blocked was brought up. But what does that have to do with Renault running with an illegal, unfair and massive advantage for 11 races in an 18 race season? They cheated for the vast majority of the season and hoarded up on points, wonder how the season would've worked out had they clamped down on them early on, just as they did with Ferrari.
It was Renault's interpretation of the rules, an innovation bordering on the edge of the rules like Williams active suspension or Brawns diffuser, hardly what you call illegal and unfair. It was declared illegal after it was approved at first, very similar to the Brawn GP car of 2009 which again was more tecnical genius (and borderline) than illegal and unfair in my book.