It's actually a few things. There are some subtle differences that are just annoyances and then some complete oversights/decisions that aren't in the best interest of the user.
Can't charge with the phone powered off
No changing the launcher (That I'm aware of)
The home screen doesn't have wallpaper options
Can't change the keyboard
The listed above are the petty issues that I have. However, they really aren't a big deal. The metro UI is pretty good and as it's designed, there's little need to set wallpaper. They keyboard is pretty good too and so I personally haven't found a need to change it. As for the big issues for me however, read on
No real file manager (That allows readabilty to all [reasonable] directories)
Ringer and media share same volume
No OTG support
No HID profile
No MHL option
A file manager is pretty essential for me as I use my device for work. Some need it, others don't. That's a personal gripe. As far as the ring/media volume, I'm not sure what they were thinking. It's been stated that this will be resolved in 8.1. As far as USB OTG support...I feel like it shouldn't have been omitted considering the lack of HID profile for bluetooth (and vice versa). Being able to plug in a flash drive or a keyboard would have been nice. However, circling back to the lack of a file manager, a flash drive would be useless. In regards to the lack of HID, you'd think this would be essential considering these devices are hyped to have Office. Without HID, again we're missing support for wireless input peripherals. And in final, the MHL. I guess that's not super important with everything being DLNA supported now. Nokia has various in house options for this as well but what if you're ever in a situation where you need to connect to a projector or something to show off that snazzy spreadsheet for work? 6 inches only goes so far...
Anyway, I'm using the device so the issues can't be all that bad. It was just an adjustment for me that I'd like to see get resolved in future iterations of the OS. The hardware is already there. I honestly think that a lot of it is to keep the line between WP and RT well defined.