I used to have the same attitude about PR that you do -- a necessary layover en route to someplace else. I've since changed my attitude, and will be taking my 5th PR-only vacation later this year. Although not responsive to your questions about El Yunque (other than seeing it from a distance), I have several PR trip reports on my webpage here: Islandtime. I've stayed once in Fajardo (near El Yunque) at El Conquistador; stayed in Rincon at the Horned Dorset; and twice sailed the SVI. Also have added many days at the end or beginning of other trips in San Juan, which is a beautiful city.

PR has the benefits of being relatively easy to get to from the US, and being, in fact, part of the US. But it is distinctly Latin in flavor and style, and Caribbean in geography. And it's a pretty big island (for the Caribbean), with lots to explore.