I'm from a rather physics heavy background and as such I'm a big fan of Newtonian spaceflight. The problem, of course, is that most people don't have such a background. The learning curve for such a system of flight can be rather steep, making games that utilize it not very accessible to the layperson.
The solution I came up with is to have the AI do the driving (with the player optionally taking direct control). That's fine if you're flying from place to place, but it doesn't work so well in combat. A thought just popped into my head to address that shortfall.
Often in Star Trek the captain will order a particular evasive or attack pattern. ("Attack Pattern Delta Two" or such). Similarly a row of buttons could be added to the UI (next to the buttons to fire weapons and use abilities) that would trigger preset maneuvers. When these are activated the AI would take control of ship navigation and move it according to the pattern.
Some Examples:
Attack Pattern Omega - Keep the ship pointed at the enemy and keep close.
Attack Pattern Alpha - Keep distance from the enemy and fly evasively.
Evasive Pattern Alpha - Run directly away from the enemy.
Evasive Pattern Beta - A zig-zag run from enemy.
The player would have the option for direct control, of course. But the attack patterns would let the player focus on using abilities and targeting weapons.