The disadvantages completely outweigh the benefits of uninstalling applications manually. Firstly being that it will cost you a lot of time to complete such task fully since every little registry key and file needs to be removed. Also the second issue comes with knowing what files and folders to delete. Manually uninstalling an application is not as simple as deleting the program files in your C:\ since many applications have registry entries to help with the functionality of the application or to add specific shortcuts within Windows. The only people that know where an application is installed are the developers. In theory it is possible for them to tell you what files and registry entries need to be removed however it would be more easier for them to create a separate process to complete it for the user (Uninstaller).
In short terms, Yes you can do it but the risk of running into problems and not being able to recover from them are heightened and unless you have a specific need to do so I would always uninstall from Control panel and run an uninstall .exe from the developer to completely remove the program since they are the ones who made the application. Either way you will have removed the application so for a user I would take the easier and stress free route of using the uninstaller.
Hope This Helps,
Josh!