As we all know the Rebel and Imperials both were not above hiring the right guys for the job. Han Solo, Boba Fett, Bossk and the rest of the boys worked for whoever had the credits. I would really love it if FFG allowed the scum and villainy ships to be useable with both current factions. They would still have to option to field a squad of just S&V but I think it comes off as more true to the source if they are mercenaries.
Scum and villainy to the highest bidder
There's true to the material, and there's game balance. I prefer balance if forced to make a choice.
Boba Fett is already in the game as hired Imprrial help.
I am definitely in the "never want to see this" camp. FFG is doing a fine job with game bakance. There is no reason at all to mess that up with faction-mixing, IMO.
Jim
The new ships can go to EITHER side. There's your balance.
FFG won't allow it in tournaments.
How about both balance and variety:
A Rebel or Imperial force that wants to employ the services of a mercenary is required to pay an extra 5 points per hired gun. Therefore: A pure S&V faction is the optimal way to play the side, but there is an official mechanic for fielding mixed squadrons, in keeping with the source material.
Who is to say that your S&V squadron...when attacking a Rebel force in a match...isn't working for the Empire? Just because there are no Imperial ships present, doesn't mean you weren't tipped off about the poorly defended supply yard with lucrative items being staged with a very light Rebel fighter escort by the Empire...
However, flying together would be more problematic. Even aside from 'Lone Wolf'-upgraded ships...your fleet has to communicate with itself. Configuring IFF codes for the computers, managing comm signals, defining chain of command (for control of the squad if/when pilots are lost), protocol for dealing with friendly casualties, overall strategy for the battle, etc...
All stuff that an omniscient player handwaves away, but as the saying goes - 'amateurs study tactics, professionals study logistics'...the "in reality" part of a functional military that can go into battle with hope of victory means you DON'T mix mercenary forces in alongside your professional forces. They get their own units, and go into battle on their own missions.
(It's one of the issues I had with all the other bounty hunters appearing WITH Boba Fett...and even he's an outside case. However, one could imagine he has a long-standing, working relationship with the Empire - so, as someone who has done years of contract work for them previously, he is probably well integrated into the necessary systems, processes, and structure - so as to be able to fly alongside them.)
The S&V faction, though...won't have that. (FWIW, you could always simulate, that - have another player fly those ships. Three players - 100 pts for the Rebel fleet, 50 pts for an S&V fleet, and 50 pts for an Empire fleet, have the Empire and S&V try to fight the Rebels meaningfully...you'll quickly see the problem! 
)
How about both balance and variety:
A Rebel or Imperial force that wants to employ the services of a mercenary is required to pay an extra 5 points per hired gun. Therefore: A pure S&V faction is the optimal way to play the side, but there is an official mechanic for fielding mixed squadrons, in keeping with the source material.
That gives me an idea for a campaign!
A 100pt build with an auction beforehand! A decked out Boba (or whom ever) is autioned off with points before the squads are built. The winner has to make a list with the remaining points. The loser makes his list like normal, but may have choice of some other thing in the campaign. He can choose all the gun or asteroid placements or something.
Actually... Auctions sound like fun in general. Offer two or three items and auction before the build. Illict items in an auction for the other factions!!
Faction mixing would make balance difficult and would make it difficult for FFG to make Scum ships. e.g. If there is a Scum ship with a droid slot, then Imperials may use it to gain access to droids they would not otherwise be able to use. That makes FFG think twice before releasing such a ship as it may be used by Imperials as well.
For competitive tournament play it's probably best not, otherwise it tends to reduce list variety not increase it (from my experience with other systems, at least). But for friendly play, campaigns, etc, if everyone's happy I don't see why not.
There can be quite a focus on these forums on tournament play at times, so don't let that discourage you from trying out what might be a good idea for anything outside of that small part of what makes up this game.
Cheerio,
Ben
Already did a thread on that concept. (Just some clarifications such as Boba Fet cannot be played in a Rebel Squadron.)
Just thinking of a good way to ease in the 3rd faction to X-wing and the one thing in mind is allowing the 3rd faction to act as a mercenary faction where you could play ships from the 3rd faction with your imperial or rebel squadron. Just put a point limit on how much you can spend on mercenary ships and upgrades you put on those ships in your squadron. I think this is a nice mix in point value.
Squadron point total, S&V Ship limit (points for upgrades on S&V ships count to mercenary limit).
100+ points, no more than 40 points on mercenary ships.
75-99 points, no more than 30 points on mercenary ships.
60-74 points, no more than 20 points on mercenary ships.
Less than 60 points, no more than 15 points on mercenary ships.
The advantage is that it makes it easier to play with 3rd faction ships instead of trying to buy every ship that comes out or buying 2 and having to point overload them just to play the new ships. This will allow 3rd faction ships to be played without having to purchase a whole new starter set.