It's an interesting discussion topic, both for SP and MP levels.
My habit is to start with the traditional 8 skills and then place any others at the end. Since walkers or batters often replace bombers for the function of removing blockers, I put them in the bomber slot if bombers are absent (e.g. Little Viennese Waltz). It's also fairly common that a level has all the classic 8 except floaters; then I either put something else in the floater slot (Goblin City) or move climbers right and leave the leftmost space blank (From the Other Side). If a level has both builders and platformers I put them together and shunt the digging skills along one place; if there are only platformers, of course they usually go in the builder slot, unless putting them with the miscellaneous skills makes a neater pattern (You only get one bash at it). However, on the rare occasions when I'm using all 12 of the "modern 12", or 11 of them plus one other, I put them in "modern 12" order.
I also like the feature that you can include a skill but give zero of that skill; I use this to emphasise that a particular skill is absent (Thomas the Climber, floaters); on the hard version of a level, to emphasise the removal of a particular skill from the easy version (Lixster Quadrille, floaters and miners); very occasionally, to create a pattern (Cry for me, which originally had 42 climbers, creating the pattern 42-10-4-2-1-0).
Anyway, getting back to multiplayer. TM and I have agreed to be each other's training partners, and had our first session last night
It was a success, overall, though a few points stood out. TM already mentioned not being able to see the skills before play. One round was a failure because TM thought the builders were platformers, leading him to take an inferior route; this ended up being not much fun for either of us, and a lot of time was essentially wasted. On the same level (Rubix's King of the Castle) the exits are so high that the lix icons indicating which is which are off-screen; of course it was easy to guess that each group of lix would be assigned to the further exit, but not knowing this for certain made things awkward, and made it easier to forget in the heat of battle.
So far, my favourite map is Rubix's Crossover Combat, although TM handily beat me on that one by digging potholes in my route in too many places