Two different stores for the same apps

When I bought my own iPad I was exultant to see that many of my apps were already Universal, ready to run decently on both iPhone/iPod and iPad screens. Opening iTunes and having my huge and freaky collection of apps and games made, surprisingly, much sense. For once, that "Applications" section on the left side menu was more than necessary stop to update my beloved library. The way they are displayed help you to get understand which apps can actually run on the iPad on a native mode, a mammoth task using the AppStore description system.
Despite my initial concerns about installing only Universal or iPad apps on the big device, new purchases would sync automatically without my consent, wether they are supported or not. Perhaps iTunes wants to be nice again with me set this behaviour as standard, so I don't forget to check out that just-bought app even if it was originally meant to be on my iPhone. Well, I can't be too angry about it.
A post last by Julio César Fernández on the Spanish AppleWeblog highlighted something that nobody really seems to be complaining about. In a nutshell, the author believes that applications that haven't evolutioned to the Universal form factor but are available as independent iPhone and iPad titles are nothing less than a rip-off. Stop to think about it. You get the uber-popular Angry Birds, which has stayed longer than iDracula, Pocket God and Flight Control on the number one AppStore best-selling spot, but is still available as an ad-hoc iPad special version on the iPad for a mere £2.99/$4.99 when the success hit has always been at the lowest price point possible: £0.59/$0.99.

By no means I want to imply that iPad apps and games shouldn't be priced higher than its iPhone counterparts. In fact I'm against iPhone apps being priced so low (see the related post about the war on £0.59 apps.) In fact I understand that there is a higher development cost to adapt a released version for the iPad and remake all the resources match its resolution. 
"The real issue comes with the Retina Display. Since more and more games are being updated for the new Apple resolution at a free cost, it makes me doubt about some developers' intentions pricing differently the same apps for the iPhone/iPod than the iPad. Is it something different or just the same thing with an HD label?"
I imagine he situation: The designer has to go back to a project already finished and upgrade all the graphical assets for the Retina Display, meaning in most of the cases improve previous work and details that weren't visible in the previous version. Annoying job. I imagine the same graphic designer being commissioned the iPad version on the same work already finished, which at least has a novelty factor and can use a bigger screen to improve the user experience.
Have you been in  a similar situation before? Wether you like it or not, a 960x640 Retina resolution doesn't differ much from the iPad's 1024x768. Running those games, because I'm pointing at game developers, is not as lame as it used to be when we did it on the iPad's screen at 2x. Should we have a single AppleStore of Universal apps? Probably not, but we shouldn't have one with HD and "for iPad" versions only.