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I watched a few episodes of this series in the 90's or 2000's, I'm in France so I'm quite certain the series aired earlier on US channels.

The main character was some sort of ship captain battling against some villain on a mostly destroyed planet. I remember the fighting scenes on screen being very reminiscent of Star Wars IV and VI when they fight in and around the Death Stars, ships zooming all around and firing while manoeuvring through half-destroyed scaffolding with turrets everywhere. It usually looked like a mix between the famous trench run and the half constructed second space station.

I think they used early CGI for the cartoon, not only the fight scene but for the characters and maybe even the landscape of the planet, but I could be mistaken.

I also remember that they sold a toy ship, that must have been the ship of the main protagonist, but I'm not completely sure, that was advertised as allowing you to take part in the battle. I believe it had some sort of sensor built-in and would react to shots fired on screen by making the figure of the pilot pop out of the cockpit.

This wasn't a cartoon (there was some CGI overlap but it was basically live action), but in the late '80's there was a sci-fi show called Captain Power and the Soldiers of the Future.

The show involved humans using high-tech "power suits" to fight a global empire of robots led by a cyborg named Lord Dread. It had a toy line as well, including toy fighter jets you could point at the screen and zap the bad guys, if I remember the commercials right the figures on the screen could zap you right back. The trench scene you described might have been the end credits.