The only thing I can think of is that because of their size, some HLEs may not be as generous with upgrades, simply because they don't have that many cars. Whenever I rent F from SFO for example, I almost always get an H car, and I have more leeway in asking for something else since they have a large fleet. With an HLE, I usually only get YF or G (and sometimes H), because they're more limited in what they can give me.

With that said, at an HLE, the service is more personal and the pickup/dropoff is more convenient. ^