To be fair, prior to the release of FireRed and LeafGreen, Meteor Mash actually was the signature move of Metagross.
Otherwise, your point regarding Sceptile's current access to Leaf Blade, and the lack of access to Blaze Kick and Muddy Water for the respective starters, is notable.
Niantic has demonstrated the ability to establish conventions and then break from those conventions multiple times and in different ways. Maybe the Torchic and Mudkip CDs will incorporate a twist to them, or maybe not. Only time will tell.