Since we're moving towards the new graphics and mouse controls, I'd like to suggest two small things that always made a little harder for me to understand what is happening on screen at a glance:
1- I would suggest to lower the rate of the blinking effect of characters and objects while still to show everything that shares the same tile. This in particular for moving entities (dwarves, animals, creatures,...). I think my main difficulty was that there is a fairly long time (maybe half a second?) where a creature is not visible, and that, alongside with a busy fortress and over many creatures, makes it difficult to have an idea where everybody is at a given moment, at least to me. It might be worth to try to tinker with the timing of the blinks, maybe reduce the time a creature is not visible or increase the time where it is (since they are the "focus" of attention of the game), so there is a "breathing room" for the eye to settle on the position of everything before seeing other entities on the same tiles.
2- Unlock the camera movement from the grid. I don't know if this one is easily achievable or not, but just for the camera, if it was possible to smooth the movement, that would also help in visualizing everything while moving around the fortress. This basically comes down to the question if it is possible to visualize a fraction of a tile or not.
These are small changes, and the first one is the one I really would like adjusted, since I always found the constant rapid blinking very hard on the eye.
I don't know if anyone else shares my feedback, but I hope it to be helpful in view of the new version of the game.