I find it odd that anyone is saying or implying that McLaren or one or more of it's employees are favouring Button.
The final(ish) design for the season was unable to be tested fully due to weather conditions.
The first two free practice sessions were marred by the rain, no proper testing could be carried out, there was insufficient usable time for the team to test everything in FP3. The was so little useful data that the team did not even know how much fuel the drivers were going to use, having to tell the driver to go in fuel save mode after about ten laps showed this. Similarly they did not know how long the first set of tyres would last on a full(!) load of fuel, on the BBC coverage one of the presenters said that up and down the paddock there was talk of nineteen laps.
When the tyres began to go off the team had to make a quick decision, did they bring the two drivers in on the same lap and take a chance on there being no problem for the first racing pit stop of the year, or should they bring Hamilton in a lap late. As it turns out WITH HINDSIGHT it would have been better to have brought them in together. I can only imagine what would have happened on here if both drivers had been brought in together and Button's wheelnut had acted the way it did in China.
The second stops they took the chance, bringing the drivers in together with very little, if any, holdup for Hamilton. They were just unlucky with the timing of the safety car.
In Malaysia we saw the sequence of messages between the pit crews and the drivers. Much seems to have been made of the fact that the wording to the two drivers was different. Well, presumably the drivers and their crews talked before the season even started and sorted out exactly how the messages should be structured. If they did not then that is the fault of the drivers for not making it clear what information they wanted.
At the first stop what the sequence showed was that Hamilton had first choice, being the leading river and said no thank you, I'm OK. Button was then offered the choice and took it. At the later pit stop Hamilton was left out as long as possible in case it rained again in which case he would be a pit stop up on his rivals. It didn't, so he was called in before he was in danger of losing a place later. He didn't.
In Q3 in China Hamilton went out fairly early to get a banker lap in, he was going to do another lap later in the session where he could go all out for it. Button was only going to have one go, so he was delayed to allow the track to rubber in further. Unfortunately the track temperature dropped, making it slower than earlier on in the session (see
http://www.formula1.com/news/features/2012/4/13227.html ) so Hamilton aborted what was going to be a slower lap whist Button had to complete on a slower circuit.
Then during the race at the first stops Hamilton was dropped in to some traffic, behind Kovaleinen and Ricciardo. It may be that the McLaren team thought that it would screw him up being held up behind such redoubtable car/driver combinations on well worn tyres, but unluckily for them Hamilton got past Ricciardo on his out lap and Kovaleinen pitted before the end of Hamilton's second lap (yes, it is irony). We all know what happened later to Button.
Overall I see no sign of bias, the only driver to really suffer was Button and that was just one of those unfortunate things that happen in motor sport.