There are a few reasons to avoid using the registry for standard application settings. Keep in mind that I'm talking in general here, not specifically about your program:
1) It is not user-friendly and can actually be user-dangerous. It is not uncommon for users to move a program to a different directory, a different computer, or to share their settings with another user, and one can't simply copy and paste registry entries like they can a settings file. Should a user want to edit/move/share their settings, they have to delve into regedit and that can be dangerous because one small mistake made by a person that isn't familiar with regediting can bork a computer in ways both small and large.
2) It was never intended as a dumping ground for third-party info. The registry was created because the OS information was getting to large to store in the old win.ini file. To allow programs to interact with windows settings and systems, such as registering file extension associations, the registry was made public. However, this allowed everyone and their brother to dump their settings in there also and, as a result, the registry is now suffering the same problem that the old win.ini did, it is getting too large and is actually slowing computers down.
3) It is an outdated model. The standard method for program settings storage is files, be they ini, xml, or json. The use of the registry has been outdated since at least win7 and even possible win xp. As with all things coding related, it is best to stick with best practices and not to fall into the trap of using outdated methods. Personally, this is enough reason in itself to avoid storing application specific settings in the registry.
4) It is an unnecessary separation of parts. If you think of a program like a house and the settings are your car, then storing the settings in a file in the program directory is equivalent to parking your car in your garage. Storing the settings file in a directory in My Documents (like terraria does with world files and many other programs do with settings and other files) or similar location is equivalent to parking in your driveway or in front of your house. While storing settings in the registry is like leaving your car in a public parking garage several miles away from your house. In the former places, the settings car is obviously part of your program house to anyone that has business looking, while someone would not only have to know to look in the registry garage, but would also have to know exactly where to look or what to look for. Again, it is just bad practice and obfuscates something that should be as intuitive as possible.
I hope that all makes sense. Obviously, you are free to do as you want with your program, I'm the last person to think otherwise, but these are some of the reasons that I recommend against using the registry for anything other than registering something with the underlying OS, such as file associations.
Serialization/deserialization really is just one of the greatest things since sliced bread, so even if you go with the registry or something else for this, I would strongly recommend getting that tool into your toolbelt, as it has come in handy for me so many times over the years. If you run into any problems or have any questions, I love talking code so don't be afraid to drop me a PM or to post in the, underused,
TCF Programming Group.