just a note as universal app developper. It's hard to create a good app for iphone and ipad. Due to the difference in resolution and power. If you want to have a polished version for iphone and ipad, you need to do a lot of tweaks for the graphics as mentionned above but also for performance issue sometimes (for example an animation will be nice on the ipad but not on the iphone because the iphone has less cpu power)
So I went the easy route, I've made my app for ipad but keep in mind that it should run on iphone...basically I compute a ratio between the ipad screen resolution and the device the app is running on, and use it to display things....But it is really not optimal and the graphics are realyl not nice on the iphone when everything is scaled down. Another issue is the user interface, optimal user interface is really different according to your screen resolution.
So I won't release it as universal app because the user experience is not good on the iphone, and I don't want have bad rating because of iphone users (yes ratings are merged for universal app and that's a problem!). But from a business point of view, the iphone market is so large...it makes sense to adapt the app if it is possible.
so finally to answer the question, I think that doing two versions is better (at least for an indie dev that has no time to polished iphone and ipad version). Perhaps releasing first a version on ipad or iphone, and then releasing another one is the best (at least for me!)