Well, they could do the exact same thing Pokemon Zeta/Omicron and Insurgance did: Add items [A machete, a dolly, a torch, etc.] to replace them, then go the S/M/US/UM route and make the HMs into TMs.
Another option is have the relevant Pokemon? Go hard!
I refuse to believe a Scyther, who literally has FRICKIN' SCYTHES FOR HANDS needs a SPECIAL MOVE to cut a tree down. Suck my ass, Gamefreak.
Actually, edit: Even better reason: Lapras. How does the LIVING EQUIVALENT OF A FERRY need to learn how to do the EXACT thing Areus created it for?! Gaaaaaah!