Once I click to run minecraft a small window appears saying "Downloading runtime", then three other folders appear onto my desktop: Game, Native Log, and Runtime. This really annoys me, as I have to keep deleting them after I am done with a session of minecraft. Why is this? It never use to happen before.
It sounds to me like you are running Minecraft.exe directly from your Desktop. The desktop is generally not a good place for executable files, and you shouldn't do that.
To fix your issue, you will have to move your Minecraft.exe somewhere else. I suggest you either move it to
%appdata%\.minecraft, where the rest of the Minecraft files are stored. Or create a new folder somewhere, such as
C:\Games\Minecraft and move it there.
Afterwards, create a shortcut to the exe on your desktop, e.g. by doing Right-Click > Send to > Desktop, or Right-Click dragging the icon and selecting Create Shortcut
You want the older version, they now include the runtime and a few other things. The version you want is the older version which requires Java installed already.
You can get it from here: https://beta.minecraft.net/en/download/
Please note this may change, but I've attached a screenshot to highlight as I had issues finding it since I only glanced for a few minutes.
You can create a bat or sh file that will have the program run into a different directory: Second Reply.
If you don't want to do that, you can symlink the directories.
For me, I had a similar problem with my computer. You can either move the minecraft executable to the
(Check where your Java path is leading to, it shouldn't be heading to your desktop)