Well...my thoughts on a few things:
If you change the default max I'd suggest no more than 6-8 but make that depend on the mission profile. Some misson set ups can be completely voided due to piloting skills of one team over another.
Now granted I've been out of the loop for longer than the game was supported offically....so please bare with faulty memories. One of the issues I recall was, the Demios mission IIRC ...I know it was one of the protect/destory cruiser missions, you could comepletely ignore your cap ship and just rack up pilot kills and win the match everytime due to point count on the caps being seriously under balanced.
Another trick was using the Ery with full load of Kysers and simply long distance gunning transports while another team mate covered you and two others went toe to toe with the enemy.
Luckily we shouldn't have to worry about the old "lag bombing" tactic anymore.
So I'd say one of the biggest things to flesh out, aside from the basic hosting/scoring system, would be mission design. Once you have a set group of missions you can then talor rules to account for possible "illegal tactics" in said missions.
I do agree that some sort of verification system needs to be in place since everythings open source now. Even down to simple table editting needs to be the same for everyone one playing in each and every match.
Random thought: instead of simply a node map that we had in the old days, how about several node maps? Each map is it's own "quadrant" for lack of a better term, each one a different tier in the competition. Once a squad performs well enough to control a certain number of nodes in quad 1, they get moved to quad 2, same for quad 3 which would be the top squads fighting for control. This would allow for a good blend of competition among newer, less skilled squads and upper level squads.