Is there a way to change what enemies you fight without clearing most of the game types?
I tried the normal way to fight ToD guys but it cleared most of the game types from the menu.

Activities can be scripted now.
The reason why it clears out is because when you load a different activities, it doesn't load up those missions.

If you want to change enemies in missions such as One Man Army or Massacre, then go copy the entire activities.ini and the script file it refers to and copy it into the different faction file.

Don't forget to change the path of the activity you're editing.
Then edit the Lua file to allow different enemies and guns.