The caves tend to be straightforward in Pokémon. The only cave I usually have trouble with is the Wayward Cave in Sinnoh, but, once you find Mira, the cave becomes very easy. Speaking of Sinnoh, the caves and forests in Sinnoh tend to give you NPC aid. In Iron Island Riley is by your side the whole time. The only really complex caves are Mt. Coronet and Victory Road.
1st gen didn't have "too many caves". I'd say it had just the right amount. Mt. Moon, Diglett's Cave, and Rock Tunnel are all straightforward. Seafoam Islands involves a puzzle, so it's less boring than all water. And Victory Road... is a cave in all regions. I'm surprised you complain about 1st gen's caves when Johto for example had more complex caves. The Whirl Islands, Mt. Mortar and Dark Cave weren't necessary to complete the game (in SS Whirl Islands is) but they were tougher to navigate than any of Kanto's caves.
Hoenn has a decent amount of caves, too. Meteor Falls, Fiery Path, Shoal Cave, and of course the underwater bits.
Water isn't Hoenn's only problem. Lavaridge is insignificant once you beat the gym, but to go back to the city you need either Fly or to climb and descend Mt. Chimney all over again. Poor design, when a story roadblock could've solved it. The two bikes are cool and all, but having to go back to Mauville to swap them everytime is horrible. Sinnoh solved this with the gear controls. Finally, Sootopolis is a creative idea for a city, but again you need Fly or Dive (and, with Dive, Surf) to reach it, which is impractical.
I'd say the problem everyone had with the water in Hoenn was a big reason why the following games didn't have much water at all.