I updated my post from page 1 with some new thoughts, rather than forcing anybody to go back here it is again. If this violates anything Mods please change.
I am disappointed that Merc units will have to align with a faction at first but the rest of it sounds ok.
Edit:
I have had some time to think about this further and I fully understand that a full contracting system is too much to bite off at the moment, but I also recognize that a lot of units take pride in their status as a Merc Unit and will take um-bridge at having to choose a faction even if they do have a preferred faction they will play for. So what I suggest is (I will limit this discussion to IS units because I fail to see how Clans would use mercs but it would work for them as well):
SPONSORED UNIT STATUS.
-At the start of each season a Unit leader will elect to play for the Merc Faction. Once this is chosen you are locked into to playing as merc the same as any other faction.
-After this the unit leader get a splash screen showing all the houses and their bonus with a check box, selecting one gets you sponsored by that house for a period of time during that season. Lets say a week. When this happens the units faction tag changes from our familiar friend to one reflecting our sponsored status (excuse my art skills) Davion in this case
This would obviously have to cascade through to all the unit members but that function should already be in place.
-once you are sponsored you can only play for that faction the same any faction player.
At this point you would effectively be a faction player whilst retaining your merc status.
What do I get?
-all players belonging to a sponsored unit (in CW matches only) would get a 10% cbill bonus to in game earnings but do not get any other bonus's that regular faction players get such as cheaper faction specific mechs
-loyalty retainer, for every week a unit stays loyal to their sponsor they could get and additional 1% bonus (upto a maximum of say 20%)
At the end of the week the unit leader then decides to stay (do nothing) or get sponsored by another house.
It could get very interesting here as the Sponsor bonus could be used to get merc units to move to more active fronts.
Example: Davion is rampaging through Liao space. Liao doesn't have enough players to defend all the time. Increase the sponsor bonus to 20% to get more mercs to sign on with Liao. Similarly you could do the same for the FRR against the clans.
Addtionally you could allow units to break their contract in less time than the week stipulated at the cost of Cbills from the unit's coffers, say 5 million Cbills the first time and escalating from there to stop units changing sides every 5 minutes.
Most of the tools to make this happen should be in place or on the drawing board, It requires about 10 minutes from an artist (new icons) a new splash page in the UI for choosing a sponsor and a bit of data base work tracking who is doing what which should be mostly in place anyway.
Just my thoughts, you could do much more but lets keep it simple to start with.