Agree 1,000%
I have the Nexus 6P, and very happy with it, running a great 7.0 custom ROM, but even with all the tweaks, and kernel optimizations, and settings made battery friendly, I only get like 5h to 5.5h Screen On time. Which isn't bad, but not great. To me IMO, if I can get like a steady solid 7.5h to 8h Screen On time, now that's amazing, but very few phones offer that, except with like 4,000mAh sized batteries.
I if was building a new Nexus or Pixel phone, or heck the OnePlus Four, I'd make it a 5.5" screen, but for sure put in a 4,000mAh battery, and then have the smaller version, maybe a nice 4.8" screen, but put a good sized 3,200mAh battery in it.
Look at the Galaxy S7 Edge, it has a 3,600mAh battery, and is probably the best battery friendly Android phone this year, besides some more niche market phone with a large battery and lower res screen. But for a flagship, you need at least a 3,600mAh battery to get great battery life. I think the Pixel XL should have come in larger than 3,450mAh.