If the Apps have a separate iPad HD app. Progress and achievements don't match. So not only do you have to repeat work... achievements don't compare with friends.
If I really must have such an App. I buy the iPhone version. Play it 2x'd on iPad. Retina apps on Retina IPad don't look bad. Then acheivements match with Dad and a few friends who only have iPhones.
It amazes me there are still third rate illiterate devs that haven't read about Universal Apps and iCloud sync.
Like Cut The Rope. iPhone version, on it and iPad. It syncs, achievements all match friends. And really, Retina phone graphics on Retina iPad, no negative impact in play-ability. It's aweful on an iPad 2 though.