I was working on an example and noticed that the .Rx , .Ry, .Rz expressions aren't working as intended and returning radians instead of degrees, ill get around to fixing that guys, sorry! stuff slips by in such a big update.
1) currently you can't have two Q3D instances at once per project (sadly), there's a good reason behind it but ill try to do something about it in the next update, it just doesn't work but it would be a performance killer if it did as you mentioned.
HOWEVER you can totally make something 2.5D using Q3D alone by using textured planes as models and making the camera orthographic (or perspective and orienting the planes to look at the camera, which is relatively easy to do). Texture animations are supported on "models" for all supported texture types using the same kinds of actions as sprites with a bit of added complexity for managing different texture types, so you could animate the diffuse map and even easily implement Normal maps / Specular maps etc. to have real 3D lighting on your sprites. You could do some pretty cool stuff that is difficult to do in construct itself. The main caveat is that collision polygons aren't supported so everything uses bounding rects in collision tests. you could work around this by making 3D objects containers of sprites if you want the collision features of sprites though, so its not a huge obstacle.
As a bonus you could have stuff layered with 3D stuff for something isometric using the Zbuffer and avoid all the headaches that make iso stuff hard.
I do want to get a 2D sprite/billboard object into the next version that works identically to constructs sprites, with extra 3D features so that it can really live in the Q3D context yet work exactly like a sprite you're used to.
2) That features always been there, you can scale it up and make it all pixelly. although the sampling will be linear unless you use the inside mode which renders to a texture inside construct.