Electronic – Why does PWM create lots of EMI and signal ground noise

I think you're on the right path, a couple of notes,

1) With a signal trace between two planes, the return current will split between the two planes, even if one of the planes is split. The return current cannot "see the future" and decide ahead of time which plane to return on. It will return above and below the trace until it sees the split at which point is says "oh crap!" and pays you back by possibly causing you to fail FCC testing. So you want to avoid running traces over plane splits even if another adjacent plane is not split. You can deal with splits with capacitors and such but this type of solution is less than ideal. I'd focus on always avoiding running a trace over a plane split on an adjacent plane.

2) Wide return paths on DC signals don't really matter.

3) You asked about two signal layers sharing the same plane. Usually, this is not a big deal if done properly. What many people do is use one of the layers as a "horizontal" signal layer and the other as a "vertical" signal layer so the return currents are orthogonal to each other. It is very common to route two signal layers for each plane, and use this horizontal/vertical technique. The most important thing to remember is to not change reference planes. Your setup could be a little tricky because going from the bottom layer to the 4th layer adds another return plane. More typical 6 layer boards are

1)ASignalHor 2)GND 3)ASignalVer 4)BSignalHor 5)POWER 6)BSignalVer

If you need smaller additional planes, like under the micro, these would usually be placed as an island on one of the signal layers. If you need to use more power planes, you might want to think about going to 10+ layers.

4) Plane spacing is important, and can have huge impact on performance, so you should specify this to the board house. If you take the example 6 layer stackup I mentioned above, spacing of .005 .005 .040 .005 .005 (instead of standard stackup with equal distance between layers) can make an order of magnitude improvement. It keeps the signal layers close to their reference plane (smaller loops).

Interspersed signals with grounds or rails is best for EMI and crosstalk purposes, so your option 1 is better here.

However, in your example you have seven ground wires and only one wire for each power rail. Assuming your signals are mostly logic level, i.e. 5V rail, it would be preferable to reduce the ground lines to four and add three more 5V lines. This will help balance the return current paths for both signal levels.

^{simulate this circuit – Schematic created using CircuitLab}

Note, with your current setup, when the signal is high the return current is through the shared grounds, when it is low, the return current is through the single wire. Add more signals and the single wire must share all those signals and noise will be seven times more significant on the rail wire.

If the other rails are driving significant currents you should also increase their counts appropriately to try and balance the currents over the available wires.

In addition, as analogsystemsrf mentioned, if the cable is of any appreciable length, it is prudent to slow down the edges of logic signals passed along the cable. Your signals may be low frequencies, but those digital edges are not.