I must echo the above sentiment "forcing player behavior is never a good thing". I have also experienced that guild experiences are not always a good thing. If you restrict ship comissions to some ratio of the player base, then you are just begging for power-gaming l337 DUD35 to monopolize the number of available ship comissions.
Everyone that plays STO will want to command a starship at some point. You want to marginalize some players into some sort of separate system though. I think that you need only one commission system. If players have ships, then crews will form naturally as like-minded players find each other. After all, a real player should be much better than an NPC in some position. Having an all NPC crew would be a handicap of sorts; Captains should want to recruit players.
I suggest that you make 'guilds', by whatever name, into starbases (perhaps smaller ones). Players and ships can then join this type of 'guild'. The station command (local admiralty) can offer larger groups of players available to crew ship positions, and have more ships available for the position that you want to play (and at the level that you want to play at).
Perhaps some ship upgrades are available only via starbase refits. A guild/starbase could use some sort of system (perhaps collective member prestige) to purchase upgrades that are then made available to member ships. Different guilds/starbases will then pick different upgrades based upon their preferences. The players and ships should naturally migrate towards whatever they then value in terms of playstyle and available upgrades.
If ships need to return to their starbase (Guild-Admiralty or NPC-Admiralty) after each mission or mission group, then you will have a naturally occuring social center where ships and players can find each other. Make something akin to mission terminals where players can see what positions are available to choose from and ships can see what players are offering to serve. This way players who want more combat/crafting/exploration/etc will find like minds to play with. People will bounce around at first, and then most will settle more permanently into those ships/crews that are available when they are and for what they like.
Sometimes I'll want to Captain my ship with my friends as crew, and other days I'll crew for one of my friends on their ship. Perhaps you can use a temporary grade reduction system for the duration of the mission to make things fit the command structure. If I log-on at a time that is outside my normal hours when my usual friends are on (maybe late at night, due to some insomnia), I may just use an all NPC crew for an easy mission just to pass some time.
This setup will allow solo-play, group-play, and guild-play; all at the same time to suit any players inclination at any particular moment. It will provide freedom of choice, which is always a good thing to give players. Making the use of a real player result in significant gain over an NPC will ensure that crews will be more full (and reduce the number of ships at any time), especially for the more challenging missions.
My 0.02.

And many thanks for asking for our input. /3cheers for PE