a 2D game will be 2D from the programming point of view regardless of what type of graphics you use (displaying 3d models is not that much harder than displaying sprites and the only thing that is hard about 3D rendering is the math involved in some of the more fancy special effects or optimization schemes (for an isometric or top down view this is easy, you just render whatever is in the field of view, the few objects that might be hidden behind a wall doesn't matter) (With most decent game frameworks the difference between rendering a 3D model and rendering a 2D sprite is about as big as the difference between printing an integer and printing a float using cout)

IMO the main differences are:

Pre-rendered 3D: (Sprites made with a 3D renderer really)
Pros:
* Adding detail doesn't increase system requirements. (unless you raise the resolution) allowing you to use very high polygon counts and very advanced render effects even on weak hardware. (You can let a program such as blender spend 30 minutes rendering a single animation frame for a single sprite, with realtime 3D rendering you can't spend more than 33ms per frame for the whole scene (30fps)
Cons:
* sprites that are animated or viewable from multiple directions will use more memory
* dynamic light and shadows become very hard to do well (since a sprite is flat so you don't have as much information to work with)
* dynamic animations (ragdolls, etc) can't really be done this way.

Realtime rendered 3D:
Pros:
* animations require less memory
* animations can be dynamic (ragdolls, smooth transitions between animations, etc)
* animations can be separate from the visual model and thus shared between models.
* dynamic light/shadows become fairly easy
Cons:
* High polygon counts and any form of additional effects beyond a diffuse texture will reduce performance. (and more advanced effects can require some rather advanced math)

If you want new games that use pre-rendered 3D you probably have to look at mobiles, there is little reason to use it on the PC anymore as we got enough performance these days to do high quality 3D rendering in realtime.

All game related things, movement, pathfinding, etc should be completely separate from the rendering and thus should be done the same way regardless of how you choose to display the game to the user.

can you say some newer games that use 3d pre rendered? i only know old games like baldues gate 2 used pre rednered 3.

See signature..

3d games will use pre-rendered aswell, for likes of background stuff and imposters.