I've been working our several 3D simulations and a 3D physics engine based on my work (scaling theory - Realitivistic Relativity). My first simulation Star2Atom is a very visual reply to the argument that star system orbits do not match atomic orbitals. Honestly, the response is a matter of perception. The Star2Atom simulation is a 4 gas-giant system orbiting an inner system represented by the yellow sphere (which includes the star). The system's orbits are all flat, but as the system accelerates becoming an atom, the passage of time for the system also accelerates from our, the observer's, point of reference (the reverse of Special Relativity's time dilation). As time accelerates the "entire" system's rotation plays a larger role because the orbits stay flat as the whole system rolls in it's acceleration. The passage of time difference in my calculations between star systems and atoms is 9x10^26. That's 9x10^26 seconds passing at the atomic scale for 1 second our frame of reference. With such a large passage in time, the entire systems rotation becomes very prevalent and makes the whole system a blur from our perspective. Essentially you are seeing all the system's event over 2.9x10^19 years in one second. It's actually very simple to understand. The simulation does not go to that extreme because it would not be visible on the screen and there are possibly hardware limitations, but it still represents the concept very effectively.

http://www.gpofr.com/documents/sims/Star2Atom/publish.htm

In response to other types of atomic orbits, my answer is to change the flat orbits of the star system and make them a bit more inclined and give them more eliptical orbits. A future simulation will show what I mean.