I love this idea,

I have a 2D sprite guy walking around and the camera is at a top down view.
Then I have a few 3D houses etc, looks neat.

The only problem im having is that everything is correct when its in 2D mode, but when i switch to 3D, my 2D is facing 90 degrees up from the grid. Its really hard to navigate and place 3D objects when you facing the wrong way. How can I correct this?

There really isn’t any 3D mode, and hence there’s no 2D mode.

It’s all just Unity3D.

By internal plumbing convention Unity maps the Physics2D engine to the X/Y plane. I’m not privy to how, but I assume they just map the x/y coming out of Box2D engine into the x/y of the Transform.

Default gravity is in the -Y direction both for 2D and 3D Physics. It can be changed to anything.

By default scene convention the default camera looks +Z (both ortho (for 2D) and perspective (for 3D) )

You can put sprites at any orientation you like. Remember sprites are visible from both sides by default.

You can build 3D stuff at any orientation you like.

You could point the camera in pretty much any direction you want.

Believe it or not you can even present a 2D physics game in the X/Y plane as objects moving in the X/Z plane if you like, just by making visible objects without any physics that track the 2D physics objects.

So… wot I am saying is, you CAN get what you want working, but again, I still have no idea what exactly you want.

I’m guessing he’s talking about what I posted a screenshot of below, which appears to illustrate his description of the issue with the camera being “top down” in 2D scene view and the sprites at a 90 degree angle from the grid in 3D scene view.

3D objects position very oddly when working in that 2D scene view. The way to deal with that is to always work in a 3D scene view and consider your 2D an XY plane that the camera faces. If you prefer working in top-down mode like that 2D scene view appears, just face your camera down and have your 2D on an XZ plane.