The only thing that Yale lacks as compared to NGLA is water on the perimeter. For architectural quality they are certainly in the same ball park. It would be a fun exercise to go hole by hole and I would say Yale is two up after 2.
It would probably make more sense to pair the template holes directly, and then it starts to get easier to see why NGLA is better: holes like the Redan and the Short are a walkover! But Yale does have some non-template standouts, so it might be closer in the hole by hole. Here's my take [and I am doing it live, no editing]:
Yale wins 1 & 2 +2
NGLA wins 3-8 +4
Yale wins 9 -3
halve tenth
NGLA wins 11-12 +5
Yale wins 13
NGLA wins 14 and wins match 6 & 4
NGLA would also win three of the last four holes IMO
You could make a case for Yale's 4th hole getting a half, that's a great hole, but it's up against the best Redan in the world
Maybe you could make a case for Yale's 8th hole, but again, look what it's up against
If anything this exercise made me think less of Yale! Best not to compare oneself to the GOAT.