>>58743414In Kanto it's that water route section between Fuchsia and Cinnabar Island, I always got to Cinnabar by surfing south of Pallet Town so for the longest time I never even knew the other (and intended) way of accessing the island even existed. I know a lot of people dislike the routes connecting Lavender Town and Fuchsia City but since that was ALWAYS the route I took rather than the bike route I never really disliked it too much, it just felt like it was the proper way of doing it.
In Hoenn it's the water routes, but your route leading up to Fortree is also annoying. Really pretty and visual and interesting when you first pass through but after a handful of treks through it I always grow bored, at least with the water routes I pop a repel every 250 steps and it's over and done rather quick.
In Sinnoh I think it was Victory Road, don't know if it's because I was a 10-11 year old that didn't speak a lick of English when I went through it, but it felt like it would never end and it was such a hassle.