The ventilated seats work great; they help cool you off a lot faster and you don't have to blast the air in the car at the max to get the same cooling effect. In that sense it's probably a bit better on your engine and might equate to a slight improvement in MPG.
I never even gave a thought about the perforations clogging when I bought it. Perforated leather is pretty common, and the little perforations getting clogged isn't something I've heard a whole lot of complaints about. The only things I can think of that would get in there are dirt that happens to be on your clothing (solution: ride around in your Jeep naked?), sand, and maybe leather lotion if you're not careful about applying it when you moisturize the leather. But I mean, what else is gonna get in there to clog up the system?
I vacuum my car on a weekly basis at the very least, which includes a full pass over the seats, so I'm not concerned about anything building up and clogging its pores that would lessen the effectiveness of it. I think that's part of it too; I know some people probably don't even vacuum their cars but once a month, and that's a concept as foreign to me as having a baby.
At the end of the day, I'm very pleased with the ventilated seats, and I wouldn't choose a car in the future without it. One thing to note, my mom's Infiniti M has ventilated seats, and I don't like the feature in her car because it makes a rather audible hissing sound. There is no such sound in my Jeep, and my car was 20k less than hers. I was concerned about the hissing sound when I saw that Jeep offered the feature on the Limited trim, but once I sat in the car and turned it on I was fine because it doesn't hiss, and when I drive I have music on anyway so I won't hear it either way. That was one potential downside for me that turned out not to be an issue. But again as for the system getting clogged up, I never even thought of that; maybe because I consider weekly vacuum part of a car's general maintenance, who knows.