Puerto Rico is a perfect engine. Though it's an impressive system, it's becoming more of a historical artifact as newer games utilize its mechanics in more interesting ways.
I have a fine time when I play it, but is a "fine time" what I'm looking for when I get together with friends to play games? No. I want to have fun. I respect Puerto Rico, but I don't really enjoy it.
It's an excellent game, but there are definitely times I don't want to play--it's so intense that the crowd needs to be into it, in my opinion. There are layers of nuance to the role selection that make for very interesting games. I feel some folks are a little too married to their style of play and don't like being put off it. It can get so bad in fact, that interaction drops down to murmurs about how non-optimal that last play was. As a solo game (using the Excel macro) it's a cool way to waste time at work while looking busy.