Unfortunately, I haven't been able to afford a new iPad yet (nor have I had time to drool over one at the Apple Store), but I've heard from many of you just how amazing that Retina display is. I'm not surprised. The iPhone's transition to the Retina was great, and it must be even better on a larger scale.
The most obvious drawback is app size. Those bigger graphics take up more space, and for many graphics-heavy applications, that could put them over the cellular data download limit (now at 50 MB). Universal apps specifically are taking this hit, even if they're not running with the new iPad-sized graphics on the iPhone hardware.
There are good reasons to stick with universal as well, of course. Customers like apps that run on both devices. Given how different iPhone and iPad versions of an app can be, a universal often feels like getting two apps for the price of one. But each developer has to decide for themselves whether universal is the right way to go or not.
In the past, universal was almost a no brainer, but I think as more and more devs figure out just what the differences are in the experience on the iPad and the iPhone, we'll see more and more devs (with limited resources, at least) choosing to split their apps up and run them device only more often.