Hello,
I use KiCAD and I have designed several medium complexity PCBs. The most annoying part when designing the PCB layout is the size and the position of connectors, mounting holes and pots/switches/LEDs, etc. when you haven't a defined enclosure. It's obvious but I had to mention it, because many people design the board before the enclosure/front panel of the device, and it should be all designed from the outside in.
A real-size footprints sheet is ALWAYS necessary when designing, you have to see the actual size of the components you're using to see if it's the correct footprint. Just create a PCB and add SMD capacitors and resistors footprints, SOICs, SOT-23X packages, TQFP, through hole radial and axial capacitors and resistors, power connectors, etc.
Then, the easyest way to test the PCB is to mount it all and try every part of the circuit. I usually start with power supplies like battery chargers and cutoff circuits or voltage regulators. If they are working well, then it's fine to go on mounting the rest of the board.
The hardest part is making wire connectors... it's that I hate them! not only checking the correct order of each wire but then the mechanical failure rate is often high when not done with adequate tools (always my case).
Test points are important, also a ground through hole pin header is, where to hook the oscilloscope ground to? I always had problems with that.
Make sure to have tools that allow you to use your hands to work and not to hold things. Buy or make a PCB holder, some fast connectors, self-holding connectors (I call them crocodrile hook), and an AC plug with a female PCB connector in the other end, ypu will need it.
Regarding to software assist quality, I like the easy way KiCAD footprints can be modified in-situ and not having to edit the whole component in the library editor. Another thing to highlight is the low hardware resources it needs, it won't need a NASA supercomputer to run for hours.
The negative points:
-Highlight function is not so clear, it should be an option to modify the intensity.
-Some straight traces are composed of several tracks and it's a problem to drag them as they are "too many collinear segments". They should be made as a single one once they are alligned and finished.
-We need teardrops!!
So these are the most usual troubles I come with at these holy moments. Hope being useful.