It's pretty early in the Indy MotoGP race weekend to be recognizing any trends but one quote from the press release issued today by Repsol Honda after the first practice session might be worth a mull.
Reigning world champion Marc Marquez said in the PR:
The new surface is quite similar to the one we had last year but it's less bumpy and the grip will of course improve throughout the weekend. Maybe for our bike the old layout worked better and the new corners make the lap a little easier. There is certainly more corner speed, more banking in the exit of the corner and we stay on the throttle longer - It's not like before when we could stop the bike and pick it up and go"
Yamaha has not won an Indy MotoGP race since Lorenzo's Spider-man weekend here in 2009. What Yamaha has struggled with since that period--and not just at Indy--is the M1's sluggishness when the bike is brought up from the side of the tire, and back down to full lean. The Honda does this very well and that trait has been key in why Honda riders have won the Indy MotoGP race the last four years.
As Marquez's statement above illustrates, the modifications Indy made to the track may have have negated any advantage that Honda had in the "pick it up and go" area.
This new style of corner at Indy can't hurt the Ducati either.