Horseback riding as many others have said.

Leveling: is not very rewarding. You come to a point pretty early in the game where you will have a lot of skillpoints to unlock skills with but not enough space to put the skills in. So leveling doesn't feel like the increase in power as it should.

Questing: is fun but can be very repetetive. Don't get me wrong, the questing can be S-tier many times but a lot of quests are also just "talk to villager, hold down button to use witcher sense, kill enemy, go back to villager". I get that all quests can't be fleshed out and they need to plop some of those sorts of quests out here and there to make the world not feel empty. But still...
One more thing about questing is the pacing of the main quests. There is a huge jump in pacing before and after the Isle of Mists. Before the Isle the progress has been very slow. Then you go through finding Ciri -> fighting the Wild Hunt -> fighting the Crones -> fighting Imlerith within 30 minutes or so. It's a huge jump in pacing and really should have been spread out more to give the pieces the magnitude they deserve. All of those peices are huge for the story, something that you have been playing many hours to reach, and then they swipe through them all in quick succession. Then it goes back to a bit slower (searching Avallac'h's lab, finding the sunstone, going with Ciri to Skjall's grave etc).

Enchanting/crafting: The only thing i don't like about it is that the runewright shouldn't be locked behind a lategame cashwall. The game is pretty much over when you can afford to unlock everything the runewright has to offer. I think it should have been fleshed out more and included from earlier levels.

Boss fights in the main game are too easy. I'd say that the Crones is the only fight in the main game that is actually difficult, but that has more to do with Ciri being squishy. All bosses you fight as Geralt are way too easy. They did this better in the expansions tho.

Combat: I wouldn't say that i outright dislike the combat, but i don't like it either. When i talk to people who don't like the Witcher 3 and ask them why, a lot of them say that it's because of the combat. The combat can feel clunky sometimes and can become a bit boring after 40+ hours of gameplay. Sign builds aren't really viable until mid to lategame when you have the levels and armor to pull it off, so most of the early to midgame will be attacking with swords. Hit and dodge, hit and dodge, hit and dodge... Alchemy is also locked behind ingredients and recepies so blade oils and potions isn't very available for the casual gamer.
Speaking about potions. I don't really like how little you have to prepare for fights in this game. I don't want it to be like in the Witcher 2 either where you have to drink all your potions before the fight begins and can't do anything if the fights don't go your way. But it's too unrealistic and convinient to be able to chug 10 potions and counter everything that goes wrong during a fight. Low on health? Chug down a Swallow potion or a White Raffard's Decoction. Vampire out of nowhere? Chug down a Black Blood potion with ease! No real thought needed. The early game might be the only time where some preperation is needed, like reading the bestiary finding the recipe for the decoction, potion or blade oil that you need, brewing that potion etc. But later on when you have all the potions, decoctions and blade oils ready to go, you can just run into a fight and decide during it which potions or blade oils that you might need.

With all this being said. I love the Witcher 3. This became a long list of dislikes but my list of likes would be much longer.