The actual topology of your ground system is important in cases like this. Currents don't just go away when they reach a ground node, they return to their source. What you want to do is to minimize the amount of conductor that the motor return currents share with the return current for the A/D section. For instance, the 12V return wire should go quite near the stepper driver, and for the 0V reference you can tie the logic ground and stepper-driver ground (12V return) together at just that point.
Ground connection or referencing is used when it is used because long experience has shown it to be the best choice in practice. "Reinventing the grounding "wheel"" may have its place in some cases, but usually not. In many cases there are competing aspects, but the overall best result is gained by using ground. Power distribution systems are one such example.
Mains or grid voltage systems would be safer if the system was entirely NON ground referenced, and this is the principle that safety "isolation transformers" use BUT the moment that a fault fully or partially grounds one leg of the system anywhere on a circuit then the whole system becomes lethally dangerous to users.
Note that ONLY ONE tool should be used with an isolation transformer, and the transformer should be located near the tool. Using long cable runs after the transformer and two or more tools risks a fault to ground in one tool or wiring leaving the other unprotected.
The difficulty in keeping a system isolated is in practice (which is what counts) far harder than the issues caused by grounding. Some shipboard power systems do have both conductors floating relative to ship ground (= seawater potential when you are floating in salt water) BUT and fault to ground is dangerous, as above, ad great effort is made to track down and remove any ground faults. In a land based system that was not ground referenced, any fault to ground on the same phase would affect all users on the same phase. So a whole street of houses may be affected by a fault on one circuit in one house.
Once you have a ground referenced system the safety aspects of detection and management for individual circuits are easily handled. Earthed housings provide both protection and detection, fault currents flow to ground and can be either "encouraged" to allow easy fault termination (fuses) or detected at very low level (ELCB / GFI). Ground referencing is an overall positive in domestic power systems.
Few modern systems use ground as an actual conductor.
SWER (Single Wire Earth Return) power systems were much used at one time and are still used in some rural systems. I saw one here (NZ)some months ago but they are rare. They are in fact very useful and cost effective but are generally eliminated for reasons which often do not make technical sense. The cost of providing a good enough ground connection at each end is in most cases low compared to he cost of many km of adding an extra conductor.
19 kV SWER line:
Wikipedia SWER
SWER slidehow - good
SWER video - NZ
Superb SWER slideshow / tutorial
SWER - Australian experience with application to developing country use
SWER - Wikipedia
RF signals are often "launched" as imbalanced signals against a phantom image reflected in the ground. A typical quarter wave vertical radiator has an implicit image reflected in the ground plane. The tall towers of AM brodcast stations almost all use this system. There are economies in materials used compared with dipole or other antennas, radiation pattern is omnidirectional and radiation angles are suited to direct wave communications - most audiences are near the transmitter for AM broadcast stations.
- TV receiver antennas 9the traditional Yagi designs) and long distance broadcast stations used for intercontinental news etc often use beam or similar aerials instead. The HRH delta Loop non ground referenced antenna was developed specially for and from such applications.
In systems that need grounding, techniques have been developed to provide grounds which are adequately good to adequately minimise the effects of local conditions. Ground proper is of essentially zero resistance as it is of sensibly infinite size. Connecting the local ground to the actual ground is the challenge and methods and needs are well understood for each relevant application.
Best Answer
Increasing the impedance of the system ground between various devices is a bad idea. Decouple the power supply feed points, filter signals between blocks as necessary, but keep the ground connections as solid as you can.
If you do manage to decouple the ground, like by adding inductance in series, then the noise will be even larger on all the signals coming out of that block. By allowing the ground to float at high frequencies, you make everything common mode noise, so it will show up on all signals too.