Some of the trouble I had in earlier attempts was refusing to fire employees (unless it meant going into debt) or hire outside experts, because I saw that those were things listed under optional difficulty settings. :) I did have to end up using those functions for my one victory, in the end.
I had no idea experts could be put back into their slots, since I only used them in a couple playthroughs I guess I didn't experiment much with them.
I also wasn't clear on how training worked, or rather, that the fee was the same for one slot as it was for others. I assumed that higher level employees would cost more to train than lower level ones, but didn't experiment much with that either since the high level ones were in such demand.
I did catch on that over-qualified employees reduced a project's output. What I'm not sure how to do is anticipate which levels will be needed from one turn to the next. I didn't like the idea of keeping a level 0 employee around just in case a slot for them opened up in a future project, when I could instead send them to train. (Of course I could fire them and hire a new level 0 instead, but...)
Having higher level employees increase the skills of those they work with sounds great, and would definitely have helped me a lot. What I'd really been hoping for was some sort of 'experience' system where the more projects an employee did, the more skilled they could become. Not as the same rate as dedicated training but to keep them from stagnating later on. I suppose that's counter to the theme, though! :D