Mike,
Hat off to you for stepping out and making the case for Flynn. If there was some personal invective included, this thread could be GCA circa 1999.
The man was one of the greatest routers in history. Of this there is no doubt. There are many Flynn courses that, it could be argued, are the equal of courses on Ira's Golf top 100 list but as
someone with a personal interest, I see a few major impediments to greater appreciation of his work: (1) other than Shinnecock and Cherry Hills, no courses that are
exclusively Flynn have received the cross generational media exposure that comes from hosting
repeat majors. Further depressing his exposure, Flynn was robbed of attribution for his greatest triumph at Shinnecock for many years. Likewise, Mill Road Farm was plowed under. Had it survived, perhaps his work in the mid-west would receive the recognition it deserves.
(2) Flynn's relationship with Wilson probably hurts more than it helps because so much of the work can be seen as a continuation of Wilson. You can't go to PCC, Lehigh, Lancaster or Rolling Green and not see the Merion influence. Whether Flynn deserves greater recognition for his contributions at Merion is a different story but in the consciousness of the non-architecture obsessed golf world, its all Wilson;
(3) The work is sophisticated to the extent that its merit is not immediately obvious. Maxwell's greens at Prairie Dunes are amazing and obviously so. Flynn's greens at Rolling Green are equally amazing but you can't tell that simply by looking at them. At first glance, you could argue that Flynn's greens are rudimentary due to the way they blend so well into their surrounds.
(4) Location, if Flynn's best work was spread between New York and San Francisco like AWT's, it would have received greater exposure over the decades. When so much of the Philly work is overshadowed in the national eye by MGC, PV and AGC and two of his other noteworthy courses are in Lancaster and Allentown, it's easy to see how his work gets overlooked.
(5) Flynn was working class. As great as he was, he wasn't a member of the club in the way that the other Philadelphia School architects were. You could argue that Ross was in the same boat but Ross had the advantage of the authority that came from being a Scot at time that golf was in its infancy in the US. Flynn gets none of the romantic veneer of the amateur or transplanted Scot.