I think Stanley Thompson does not get the recognition that he deserves due to most of his work being in Canada. When you play St. George's in Toronto, you quickly realize that it was designed by a great architect. It truly is an amazing routing.
Likewise, I don't think William Flynn gets enough recognition. Most of his courses are in Philadelphia, where the quality of golf is so high, that they don't get the individual acclaim that they deserve.
I also think the question is largely dependent upon where you ask it. Stanley Thompson is not under appreciated in Canada, but is in the US. Likewise, while Alison may be under appreciated in the US, he is certainly appreciated in Japan.