JC,
"Better" is always a matter of opinion. "Favorite" is, too, except how can anyone argue with your choices as that adjective is all about "taste"?
Because of the differences in the ground and, therefore, the routing (and the wind and the maintenance meld, etc., etc.), there really isn't a "template MacRaynor course". Many of the HOLES are similar, but, of the seven I've played, they all have different playing characteristics, flow, etc.
Also, no two template holes are identical and, with some them, if you didn't know what they were "supposed" to be, you'd miss them (The Greenbrier is the best example I know).
As to comparing template holes: For me, it's in the construction - especially of the green complexes and I like to use the best one I've played as my personal reference point. Redans are especially easy to compare since there's so many of them and they're one-shotters. Of course, the "requirements" of a good/great Redan can still be pretty personal but those are mostly gray areas as, without certain minimum basics, a hole fails to qualify as a Redan. As an aside, the 3rd at Merion is as good an example of that as I know. It has only one of the characteristics of a consensus Redan so it just doesn't qualify and is, therefore, excluded from all discussions about Redan holes.
But, I digress. You can BUILD wonderful green complexes (although it's harder at Fishers than on the mainland). My reference point for a Redan is, of course, National although there's lots of good one's out there so the weak examples really stand out IMO (e.g. Fishers and The Greenbriar). NGLA is also my reference point for a Road hole, a Cape, an Eden, a Sahara, a Bottle and an Alps. TOC is the only really good Long hole I know although the acreage required to replicate it is probably unrealistic anywhere else.
Par 4's and, especially, par 5's are more complicated for obvious reasons although the greatness of the Road holes at both NGLA and TOC is all about the angle of the green complex so I don't know why there weren't more good examples from MacRaynor outside of National.
Similarly, the Short at NGLA is so much better than any of the others and it doesn't need to be that way. Raynor/Banks could have done more at Fishers with #16 and, also, #17 at The Creek could be more challenging, I think.
For an Alps, you need to have a pretty good hill already in the right place for the rest of the hole (and the routing) so I'm not surprised that NGLA and Fishers are the two best that I know. I like them better than the original at Prestwick.
Old Macdonald sounds like the ultimate comparative laboratory for your question.
Why don't you send a private message to George Bahto and Tom Doak and ask them both to post? Who would know better than those two guys? Lester George is probably a an "expert" on this due to his restoration at The Greenbrier.