What I would do is replacing the app that has the most users, so to force the least number of users to delete an app and download a new one. In other words, if the iPhone app has, e.g., many more downloads than the iPad app, then I would remove the iPad app from the App Store and update the iPhone app with the new universal version.
This reasoning does not take into account the following:
as you say, the iPhone app has bad reviews, and you would keep them all; users would have the possibility of rating it again, but there would be some inertia;
you don't know for sure how many "active" users your two versions have; specifically, if the iPhone version has got bad reviews, chances are that most users have already deleted it from their devices; to have a better estimate of "active" users you could use the number of downloads your app hasd on their last update.
Hope this helps.