Don't read/store settings directly from/to SYSCONF

Instead of directly reading/storing settings from/to the SYSCONF, we
now store Wii settings to Dolphin's own configuration, and apply them
on boot. This prevents issues with settings not being saved, being
overridden and lost (if the user opens a dialog that writes to the
SYSCONF while a game is running).

This also fixes restoring settings from the config cache after a
graceful shutdown; for some reason, settings were only restored
after a normal shutdown.

Fixes issue 9825 and 9826

Source/Core/DolphinWX/FrameTools.cpp

@@ -1187,7 +1187,7 @@ void CFrame::DoStop()
     if (NetPlayDialog::GetNetPlayClient())
       NetPlayDialog::GetNetPlayClient()->Stop();
 
-    BootManager::Stop();
+    Core::Stop();
     UpdateGUI();
   }
 }