Other than keeping the miles as low as possible on it, I personally don't believe there's any advantage to NOT going to the dealer to take care of things with your JK. For one, they keep a record of your vehicle.
I don't have my JK/JKU yet, but there's another car in the family, a honda,
and we've decided to take it to the dealer, for all service.
They've mailed and called us on numerous occasions to buy the car back and/or offer us incentives on trade-ins. Now, I don't care for honda as a personal vehicle, but it happens to run smoother and more quietly than any other car I've seen lately. And, it's a 4 cylinder. I've even snuck up behind people walking down our street, only to startle them (unintentionally), as I /we mosied on by.
They've come up to us afterwards, and asked us "Is that a hybrid", etc. The answer is no, it's just a regular accord. They say they didn't hear a single sound. We're like amazed to hear that.
Not sure if that's a result of taking it to the dealer to change the oil, and what not, but this car happens to NOT burn ONE DROP of oil, between oil changes. I've never seen a honda like this. Some of them burn so much oil, there's no telling how they spend most of their lives.
I do my fair share of driving "ours", and other than warm-ups, I don't baby it. It's one purchase that the little woman has yet to regret.
So, does the dealer know something about this vehicle, that we don't?
I've suspected for a while, that there's a segment of cars, in a certain V.I.N. range, that were made exceptionally well, and someone at my local dealership, wants this car back. I don't know. But it's a 2010 model.
I'd sure like to find a similar V.I.N. range of JKs/JKUs that were similarly built.