When playing 3-player Warmahordes, Malifaux, etc., there's a fairly simple solution. As long as the playing area is a square, you can "remove" the corners to create an octagon with sides of equal length; each side of the octagon is a potential deployment zone. No player may deploy adjacent to or directly across from any other player. After determining initiative, the first player picks a side, the second player selects and deploys in one of the two eligible non-adjacent sides, and the third player deploys in the space he's been left. In this way board setup and deployment zone selection retains its importance and each player starts equidistant from each other player. The corners that were not eligible for deployment are restored during gameplay, giving the familiar 3x3 or 4x4 play area.

Also, I disagree with the notion that a scenario is mandatory. Scenarios can be great and are often better than just last man standing, don't get me wrong. Three player free-for-alls often do result in kingmakers, but striving to make sure you're the one made king introduces an interesting meta to the game that's absent to two-player gaming and IMO isn't worth worrying about.

We play 3-way and even 4-way matches regularly. If you are unlucky enough to be caught in the middle as everyone pincers in then you are toast, but we all recognize that and tend to dance around the edges for a couple of rounds rather then just blast up the center. We also tend to split our squads into two groups. Even if the two groups are working together short-term we are always mindful of the need to split one group off to cover an incoming straggler.

It is defiantly a different flying style, but the same can be said for a 300 point game between two people. Those extra points let you have a core force plus send out some heavy flankers, resulting in a lot more defensive play around the edges instead of just bashing up the middle.

I can see some 3 player scenarios popping up.

Faction 1 must defend "X"

Faction 2 must destroy "X"

Faction 3 must capture "X"

How it plays out I'm not to certain but I expect it would most likely be a small space station or shuttle as the objective.

I actually started writing out a scenario where the Imperials are tasked into defending a space outpost and 3 transports. The Rebels are trying to destroy the outpost and the transports, all the while a group of scum are trying to recover 3 transports filled with military supplies.

The Empire player is trying to prevent both objectives from happening and win if they destroy all rebel/Scum ships. If the Rebels destroy the outpost and transports before the scum can steal them the Rebels win. If the scum faction manages to steal the 3 transports and get away they win.

The Outpost would have 12 hitpoints and 0 agility. Each transport would have 5 hit points and 1 agility.

The scum can steal the transports by getting in range 1 and completing a docking action. Once docked, no red maneuvers can be taken and the ships agility is dropped by -1 to min of 0. The transport piece is in tow behind and connected to the base of the scum ship. So when you move, you move both. The rebel player can either choose to target the scum ship or the transport. Still need to figure out the details and play test it.

Need to figure out what would be a good point balance. I'm thinking the scum faction be only about 80 points, Rebels 125, and Imperial 150 with additional Tie group of 3 Academies pilots and Night Beast as reinforcements after turn 4.