To answer the question about where somebody should go to see the "purest" Flynn, I think we are fortunate in that although many of his courses have seen changes over the years, it isn't as much as most other architects' work from the 20s and 30s. The one aspect of design that is least changed in Flynn's body of work would seem to be the routings...he was that good at it and they endure because of the built in elasticity.
When you visit a Flynn course, it is hard to imagine an improved routing. I do question one hole. Why didn't Flynn make the 8th at Philly Country a dogleg left hole? He had a lot of room on the right side of the 8th fairway and then 8 and 9 would not be back to back near straightaway holes.
Two courses come to mind if you want to see them as close to the drawings and as built and they are out of the Philly area; Shinnecock and Kittansett. Even though Shinnecock has been lengthened over time, that was Flynn's intention and he allowed for it in the initial design. These two courses are really on when it comes to design integrity. Kittansett still looks nearly 100% like the original drawings and earliest aerial photographs. It still has the "interrupted fairways" that Flynn was designing in the early 20s, very much the result of the Pine Valley influence. This design tendency was often not built as drawn on other courses or lost over a short period of time.
I think the Cascades Course, CC Brookline, and Eagles Mere are also great examples of courses that are close to the Flynn construction era as they come.
As to Merion, well it is still early in the research process to make definitive statements regarding a definitive design history, it is surely fascinating and will make for good reading
. Yes the fairways are narrower but can be easily changed. It has been discussed at length that the finish and playability of the bunkers are currently different than the Wilson/Flynn era, but the locations of the bunkers, the greens themselves, and the routing are all great examples of great architecture.
Regarding Pine Valley, I don't think you can make a strong case for much Flynn design work. He was really instrumental in agronomics though and took charge in 1918 of regrassing the entire course when they lost the grasses. He added some tees, redid some bunkers, built the alternate 9th green to Alison's specs, and probably was in charge of construction of the last 4 holes after Crump's death under the auspices of Alan and Hugh Wilson.
It is true that for playing conditions, nothing tops Huntingdon Valley. It is one of my top Flynn courses and I think the best original design in the area. It would be a great venue for ANY championship from local to national (think US Open).
For bunker placement I think Shinnecock, Brookline, and Merion are tops. Alas, I would also say Boca Raton South if it were still around. For the finish look of the bunkers, I'd pick Merion 1981. As for present day bunkering, I'd take Shinnecock, Brookline, and Philly Country.
For greens and surrounds, I do like Rolling Green quite a bit-but might go with Indian Creek (even though I've only seen it through materials sent to me from Joe Pantaleo, the head super, and photos by Craig Disher). There are numerous courses where the greens are little changed, certainly Philly Country is not one of them and may be among the most changed.
For a Flynn course that is pure in terms of the use of trees, that is a difficult question. I'd like to know how Tom Paul would answer it. Perhaps Shinnecock. This was also a fascinating use of trees given the topographical differences of the front and back nines.
I'd agree with Mike Cirba. If Flynn could see his courses today in the context of changes to classic courses in general he would be pleased. He would not be surprised, he thought that much ahead and planned properly.
As an engineering effort, the Cascades was an amazing effort, but I'd go with Indian Creek. They had to build that course up from dead level 2 feet above sea level. Amazing feat!
In my view, the biggest losses to the Flynn body of work are that Boca Raton North and especially South courses and Mill Road Farm no longer exist, followed somewhat closely by the loss of the 2nd course at Eagles Mere and Opa Locka in Florida (maybe these would be in Dan Wexler's 3rd volume of lost courses in the unlikely event he was to do another).