I prefer either as long as the gameplay loop is fun. Gimme a game with broken mechanics and annoying endless grind, and I will spend a total of 0.05 seconds debating on whether or not I should cheat my way towards the gallery.
When it comes to game mechanics: 2D or even 1D (mostly kinetic visual novel). 3D typically does not properly support Linux, typically requires a dedicated video card, and typically has poor visual quality and stability problems. I really don't need that.
When it comes to the style of rendered images and videos: 3D done well is better than 2D done well. 2D done well is significantly better than 3D done poorly.
Both 2D and 3D have their own perks. 2D games are more difficult to make as they have to come to par with 3d games in respect to their gameplay experience, since 3d games are modeled in 3d-modelling software such as DAZ3D, Blender, etc.
There're few good 2d games like SummerTime Saga, Demon Deals, Milf Plaza, What a Legend, and a few more.
Even not all 3d games are good, there are few S-tier 3d games such as Eternum, Such a Sharp Pain, Chasing Sunsets, Ripples, and a few more.
Mostly i prefer 3D but when 2D is done well it tends to be better because 2D is only limited by imagination time and skill of the artist unlike 3D Daz3d being the most commonly used programme is a bitch to use for animation
3d in general. But I have played som 2d games where the story have been amazing, and the artwork have been great aswell. And if it had been 3d. Maybe it had been better? Maybe worse? Dunno. But I do know that it worked as a 2d game, and I really enjoyed it. So like so many things when it comes to comparing, you have to compare what you compare aswell