I like the water routes with the currents in Hoenn, it's a neat idea for a puzzle, but it was always so annoying to attempt it over and over because you'd have to fly back to Pacifidlog and go through all the surfing again. Just felt like a waste of time compared to even the slow sliding/spinning tile puzzles in Gen I, because at least each puzzle was contained to a room and could be figured out through carefully examining your options.
I think it's difficult to call out particular routes from earlier Gens, because they function differently in terms of design compared to later Gens where it's Route > Town > Route > Town > Route...
Rather, you have something like Violet City and Azalea Town, and then you have Route 32, Union Cave, and Route 33 between them. On its own, Route 33 can be seen as a waste of a route since the most interesting thing there is Hiker Anthony, even Slowpoke Well is part of Azalea Town, but when you consider it to be PART of the journey between major destinations, it's no longer just its own route, but a "trek", a sequence. And that's why something like Kalos Route 1 is disappointing. It's a misnomer, because there is no sequence or trek between major locations, it might as well not even exist, combine Vaniville and Aquacorde into one town.
