I talk about this quite often. The barrier of entry for 3D is higher, but in terms of production 3D is a lot faster than 2D in the medium-long term.
For 2D characters you have to sprite every frame, and each time you add an action that's new frames for all characters with that action in all directions that action can happen. In 3D it's a new animation that automatically works for all characters that share the skeleton and works in all directions due to being 3D.
With 3D you can easily zoom the camera onto a character and see their fine-movement and expressions close up. It's way easier to choreograph a cinematic effect. One example is a battle-system, a 3D camera can move around the battle stage and point at various targets and special effects. It can make battles far more visually exciting, 2D is much harder to emulate this.
For producing maps, with 3D you get real-time lighting that automatically applies to your surfaces. You make a texture, then you can scrub up a wall with that texture and add some lights to get the shading you want. In 2D you need to work extra hard with the lighting due to it not being physically accurate. 4/3 2D orthogonal perspective is not physically representable: dynamic lighting Plugins often just apply a light map to the top of the screen and multiply that in, rather than attempt to respect the confusing nature of walls, ceiling and occluded geometry.
2D has its benefits, the ability to go in and decide exactly how your game looks without being slave to a lighting system is very powerful - if you chose to wield it (having the choice alone is a big factor, I think). It's much harder to make a pretty 2D game, as with 3D you can just slap more shader effects into the scene, add more lights, increase detail on your high-resolution textures, add some physics objects - but I will argue that a pretty 2D game is far more deliberate than a pretty 3D game. The amount of labour that went into Cuphead is huge, they chose exactly how that game will look and pursued it - recreating that in 3D is very difficult - but I believe somewhat possible: Guilty Gear Xrd is an excellent testament to dragging 2D values into the flexibility of a 3D world.
A lot can be said about the merits of beautifully created hand-drawn 2D "parallax" maps.
3D also brings expectations along with its perceived visual quality; if you have extremely realistic looking characters, then most players will expect voice acting and lip-syncing. A brief look at the feedback to the game Overgrowth shows that many players feel it needs voice acting to match the characters. If you want to avoid this issue, then it is easiest to dial back to an era where 3D graphics did not carry this expectations due to limitations - but then it is very obvious when you violate these limitations. If you have PS1 quality 3D graphics, then you probably shouldn't have 2017 era 3D effects such as high resolution frame-buffers, anti-aliasing and screen-space effects. Many indie 3D games violate these limitations and end up looking like terrible 3D graphics, rather than evoking an era of 3D. It's difficult to balance.
2D does have a similar issue with expectations; if you have high resolution sprites then you should push the boundaries of what you're doing with them as much as possible, such as have sprite rotation, scaling, transparencies, special effects - otherwise your game looks visually flat and dull (like 99.99% of all RPG Maker MV games, unfortunately). The alternative is dial back to an era of 2D where these expectations don't exist - and things get a little easier with retro-style aesthetic (incorrectly called 8-bit a lot of the time) - but once again when you violate the limitations it's very obvious, I'd say a vast majority of retro-style indie games violate limitations of the platform they're trying to evoke (off-grid pixels, 2x MV assets violate this, sprite-rotation, transparency, too many colours in the odd sprite).
In both cases of these expectations, it's hard work to go either side of the line, but super easy to just be lazy and take the middle option of mix-and-match, which is what majority of indie games do and end up looking visually similar with violations of their era on one side and poor graphics on the other side.
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All these decisions depend on your project, not every project should look the same or be 2D or 3D.
Without showing off too much,
here's a sneak preview of my RPG Maker MV game that is currently in early development planning. I'm trying to push the expectations of 2D presentation in RPG Maker MV as much as possible, including the use of 3D models. I'm trying to take advantage of everything 2D is good for and avoid the limitations as much as possible - at the same time I've also got basic PlayStation era 3D objects within the 2D world and I am trying to take advantage of 3D graphics in this regard too, being mindful of its limitations (particularly in a 2D world). Personally - and I stress this is my personal opinion - I think this hybrid approach fits RPG Maker MV best.
Sorry, I'll stop messing around.
