I came up with a couple of alternative rules and I'd like some feedback:
As an alternative to the turn order, you may use this rule instead.
Instead of each player taking one turn at a time, both players instead share a turn. One round of the game would be equivalent to one turn.
During each phase of the turn, each player will take turns activating a different unit.
The player who won the initiative will always go first.
During the movement phase, players will take turns moving.
During the psychic phase, players will take turns using psychic powers.
During the shooting phase, players will take turns shooting.
During the charge sub-phase, players will take turns declaring charges. Overwatch will be fired as soon as each charge is declared.
The fight subphase goes on as normal.
Players may spend 1CP to activate one unit out of order per turn, as in the fight subphase.
All units MUST be activated by the end of the turn, even if they will do nothing. The exception is the fight subphase, where only units in melee may be activated and the psychic phase, where only psychers may be activated.
Instead of setting up a single table, you may set up any number of tables.
Each unit may be set up on any one of the boards, or on reserve, if it is allowed to. Units arriving from reserve may arrive on any table. Units from different tables may not interact with each other. When a flyer leaves a table edge, you may set it up on reserve. At the end of any of the controlling player's movement phases, it may be set up on any other table within 6" of the edge closest to the table where it was.
(I like this flyer rule because it allows you to use flying transports to strategically reposition your troops)