Eli was a better thrower of the football than Troy.
He had a stronger arm, especially down the field — able to layer deep balls over defenders with real touch, which is how he built his reputation on go-routes and back-shoulder throws. His two Super Bowl MVP runs were built on clutch, high-difficulty throws in big moments (the Tyree helmet catch drive, the Manningham sideline throw against Foxworth are both testaments to arm strength and placement under pressure).
Troy Aikman was more mechanically polished —one of the more fundamentally sound passers of his era, with excellent footwork, timing, and accuracy on intermediate routes. He wasn't asked to push the ball vertically as often in Dallas's offense (which leaned on Emmitt Smith.