I like this idea! It needs some balancing, but it make combat a little more interesting, not to mention that it could balance the little guys and the biggest of the big.
For balance, I like the idea of it being on a station, but that means that if the enemy station is out of reach you're out of luck. I think it needs to be able to go on ships. To balance this, the ship would have to stop, divert all power to the cannon (no weapons on the ship can fire, not even turrets), and after a build up period, it would fire. (Size would affect the damage output) Also, direct damage might be a bit much. You could just build a fleet of these flying Death Stars and then destroy everything in your path. Maybe something along the lines of the Hoth EMP cannon would be the most common type. That way a titan could be opened up to a devastating attack if planned correctly. Also, the cannon ship should appear on navigation every time it fires.
Now, this could make combat far more interesting. Say you have a titan in your fleet, but the enemy has a long range cannon, that means that your titan could go up in smokes if you're not careful. This would add great dimension as the titan fleet is now targeting the cannon in hopes of saving their flag ship. They send out a strike force to deal with the threat. But the cannon is already moving to a new sector from when it last fired. It could become a game of cat and mouse. The people pursuing only getting cold information while the cannon moves from place to place. Combat is no longer a war of attrition and now gives a tactical edge to the ones who maneuver and strike the enemy with planning and swiftness.
Now, how does this balance smaller ships? Well, take for example the EMP cannon. We know smaller ships cant take down titan shields, or if they can, it takes to long and you'll lose most of your ships. With the EMP cannon though, that could change, one direct hit from an EMP cannon or two could shut down the titans shields and most of it's worst weapons if the pilot makes a wrong move. Just then, your strike force warps in for maximum damage. Targeting the titans weapons and infrastructure until it's shield come back up, but by that time your battleships are engaging the titan, removing what little shields it has left, giving the smaller ships time to swing around and deal more personal damage. This gives a place and meaning to smaller ships as a small weapon capable of precision damage rather than general area damage, while not denting the usefulness of titans. EMP cannons can miss if aimed improperly, tipping them off and starting a premature fight where the titan can use full force.
Overall, a superb idea, but all this requires either a massive amount of dedicated players with good PCs or for the AI to be able to build fleets and make strategies based on the current situation, not to mention dynamic AI factions, new area control designs, and better fleet AI among other things. The idea is great, but should be a cherry on top rather than the cake itself. Once they get the base of the game laid out, I think this will make an awesome addition to an already great game.
