It completely depends on what you are making.
For example, making a 3D model of a human is much more difficult than making a 2D sprite of a human. But... Animating a 3D model of a human is much easier than animating a 2D sprite of a human. Once the model is made, everything else is quite easy in comparison, but when a sprite is made, well you might need to animate it, and that is very difficult to do at a good level.
It might be an idea to stylise - I mean look at Minecraft - anyone could come up with better visuals, but they suit the style of the game. A lot of indi developers are using retro pixel art, monochrome sprites, that sort of thing - nobody seems to really mind as long as the game is strong in other areas, like playability.
So I would say that it depends on the game. If it's a game with lots of characters, then 3D models makes sense and would save time in the long run.
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