Really though? Alonso is a 2x F1 champion and was driving for an Andretti team with 6 drivers including RHR and co. His entry being a one off entry with everything thrown at it where Coyne had Bourdais for a week then had Davison who hasn't driven since 2015 and Pippa Mann who races part-time. On team and teammates alone, you should expect Alonso to beat Jones.
During the month of May, Alonso had a whole day in total to himself allowing him to gain additional data. More track time = more experience in the IndyCar at Indy. Yes, Ed did do the other races but this is his first race in the oval spec car with Phoenix being run on the road course spec so this is a completely different spec of car to the DW12 that Ed drove for the other races. Although more time in any spec of the car is beneficial, you don't gain the experience that relates specifically to that spec.
Yes, I agree that Alonso was better in Qualifying. Although for reasons above, that was expected.
During the race, Ed sustained damage to the car by running over some debris (Read
here) causing him to pit and was into 28th. Also, the floor was damaged which couldn't be replaced losing Ed some crucial speed. Alonso didn't have such problems in terms of speed. Yes, Ed got slightly lucky by pitting before a yellow but that happens and that put him ahead of Alonso into 4th with Alonso 7th. He finished 3rd which was the best ever official result for the team. (Alex Lloyd will tell you why he thought he deserved 3rd)