Something I've been doing, and it seems to work well is:
Backup your iPhone or iPod Touch completely to iTunes.
Don't install any but the most essential iPhone apps to your iPad.
Every now and then log in to iTunes and check for updates.
If any of your iPhone apps become universal you will see it appear in the iPhone/iPad app section in iTunes....now either sync that app with iTunes or install it natively on your iPad. If it's a paid app you won't have to pay again, because you already bought it.
This way you can keep from having useless iPhone apps on your iPad until they are truly compatible. I only have a few iPhone apps on my iPad and they are mostly audio apps that display doesn't matter. I also have SlingPlayer installed on my iPad just because I am waiting for it to go Universal so I can use it again. I had Air Video installed and was so pleasantly surprised when the update came in that said iPad Support.