As well as using a batch file to launch your mod, you can instead create a Windows shortcut.
For example, you have created a mod called MyMod. This lives in its own MyMod directory below the main Medieval II Total War directory.
To use the mod, copy the Medieval II Total War\medieval2.preference.cfg file and call it MyMod.cfg (it must be in the Medieval II Total War directory).
At the end of the file add
[features]
mod = MyMod
Now, instead of creating a bat file to run the mod, instead copy your existing Medieval II Total War Windows icon (also known as a shortcut).
Right click the icon and select Properties from the pop-up menu. On the Shortcut tab, go to the Target field and add "@MyMod.cfg" to the end, e.g.,
"C:\Program Files\Sega\Medieval II Total War\medieval2.exe" "@MyMod.cfg"
There must be a space between the double quotes in the middle.
Click OK. Rename the icon to something suitable (select the icon and hit F2 to rename it).
Double click the icon to play the mod.
Thanks to Epistolary Richard for initially documenting the mod switch.
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