There are a few 3rd party tools in the unity asset store that make 2D pixel art games easier to deal with. You pretty much can't look up pixel game dev in Unity without running into the TK2D package. I haven't used it to its fullest yet, but what I've experimented with so far seems to be pretty good. There is a "pixel perfect" setting in the TK2D camera that should work unless you start messing with zoom values. I think the sprite storage is also more efficient than Unity's built-in method.
Other than that i found the lack of frame capping annoying (no way to hardcap frames/physicsupdates to 60fps from what i've learned)
I'm not sure about physics, but I am pretty certain you can cap the update frame rate as an application setting.