Generally, there should be no problems with the upgrade.
Some potential issues are:
1. Hardware issues
This can be solved by downloading drivers either from Windows Update, or your manufacterer's website. For example, I have an Acer laptop so I go to Acer Downloads to get my drivers if they weren't detected in Windows Update.
2. Driver issues
During installation, but not likey after it.
3. OneDrive(formerly SkyDrive)
If you use OneDrive then you might notice that some files synced will be "Online-Only". If you want to download it, then just right-click, "Make Available Offline".
However since you've been running Windows 8.1 for a while, then the issues would most probably be non-existent. The most likely time to run into problems is during the Upgrade.
Whether it will be just like it was installed freshly on an empty partition, well the system files yes, but your personal files no! :P
After some time, you'll get used to and love Windows 8.1 like I did! :)