One thing that I noticed was that the new iPad Mini with Retina Display (as well as the iPad Air) does not have the Touch ID fingerprint reader like the iPhone 5S. I was a bit surprised about this omission but figured Apple needed to hold something back to get people to buy next year's new iPads.
As with the previous generation, I also hate the speaker placement on the new iPad Mini. Depending on how you are holding it, the sound can appear to come from one side (or be muffled by your hand). Both the Google Nexus 7 and Amazon Kindle Fire get the speaker placement right so I can't understand why Apple hasn't figured it out yet.
At the end of the day, the new iPad Mini with Retina Display is still an iPad Mini - just with better hardware.