HG/SS Mount Silver. It was bad enough in G/S/C, but then they added Rock Climb to the list of required HMs to navigate it just because "hey, new HM introduced this gen!"
X/Y Route 13: Battling in Sandstorm + wind hindering movement + having Pokemon chase you down + Repel has no effect? No thanks.
X/Y Parfum Palace. Nice looking facility, absolutely pointless and time-wasting sidequest involving characters nobody gives a damn about, and who with one exception never show up again.
Most Victory Roads: Wouldn't be as bad if not for the mandatory HM usage. aEspecially the ones where the redundant HMs like Waterfall, Rock Smash, and Rock Climb are involved. And maybe put in a Nurse NPC or something midway through so you can heal your Pokemon? Can you grant us that much in the future? Please?
R/S/E Water routes, but ESPECIALLY the ones with the one way currents. I hope whatever game designer planned that monstrosity is in some other line of work now.
D/P/Pt: Mount Coronet. I don't have the level of hate for it that some of y'all have, but it's still an exercise in tedium and too many HMs.
D/P/Pt snow routes to Snowpoint City. Walking speed slows to a crawl and oh yeah, permanent Hail every battle.