Ferrari gets it Wrong
Ferrari tried something different at Monza. According to Alonso, they had 'nothing to lose' and thus tried a different strategy with their lead driver. They asked Alonso to extend his first stint to 27 laps(four more laps than Vettel) in order to attack late in the race when Vettel's tyres had degraded. However, as we now know, that didn't work out. Here's why.
First of all, Alonso lost way too much time by extending his first stint. He was five seconds behind Vettel when the German made his pitstop on lap 23. That gap doubled to 10 seconds after Alonso's stop on lap 27. Total time lost to Vettel - five seconds.
He also lost time to Mark Webber, who pitted on the same lap as Vettel. Alonso was five seconds clear of Webber before Australian's pit stop. That gap decreased to just one second after he made his sole stop in the race. Total time lost to Webber - four seconds.
So instead of fighting with Vettel, Alonso had to keep Mark Webber at bay for rest of the race. From there to lap 43(after which Vettel had to slow down because of the gearbox problem), Alonso set identical lap times to Vettel and Webber.
Now all he had to do was to wait for tyres on Vettel's RB9 to fall. And the gap to Vettel did decrease - to the original level of five seconds at the end of the race. However, that had more to do with the gearbox issue which Vettel encountered and less to tyre degradation.
Mark Webber encountered a similar issue in the sister Red Bull that prevented him from overtaking Alonso. However, unlike Vettel he did have the advantage of DRS to retain the gap till the end of the race. Without the gearbox issue, Mark Webber would have easily overtaken Alonso.
Note - One thing Ferrari could have done was to extend Massa's first stint and use him to slow down Vettel, who now was on fresher tyres. Instead they pitted Massa on lap 24, one lap later than Vettel and all Vettel did was post laps which were more than a second quicker than Alonso.
Hamilton - Forced to Revert to a Different Strategy
After qualifying in 12th place, Lewis Hamilton started the race on a different strategy. The idea was to do a long first stint on hard tyres and attack at the end on faster medium tyres when everyone else is on the hards. But those plans took a bitter blow when Hamilton encountered a slow puncture and he had to pit on lap 13 and subsequently switch to a two stop strategy. Until that point he wasn't looking particularly impressive, probably due to combination of slower prime tyres and higher fuel loads.
Hamilton then did a 25 lap stint on medium tyres where he was really strong, setting multiple fastest laps at the end of this stint. During this stint, he ran as high as fifth before making his final late stop on lap 38. In fact, he could have stretched this stint but with all the radio problems, Mercedes didn't wanted to take the risk of falling off the cliff.
The timing and length of the stint clearly showed that Mercedes actually had the pace. The fact that Hamilton was on a two stop strategy and Rosberg finished not higher than sixth gave a general misconception that Mercedes lacked on outright pace in Monza.
After his second stop, Hamilton came out in 14th place and faced an uphill task to return to points. He then put on some spectacular moves on much fresher tyres to finish in 9th place. However, drivers in the past have finished much higher from back of the grid, albeit in different conditions, and that was the only down point about his performance.