Gears of War has tighter and more refined shooting mechanics, whereas Uncharted has stronger writing (which isn't saying much when compared to Gears of War) and elaborate set-pieces.
The single-player in the Gears of War franchise kept improving with each subsequent game, but the multiplayer has been uneven. The original Gears of War had great maps, but the weapon balance was terrible (the shotgun dominates almost every match). Gears of War 2 had somewhat better weapon balance, but the overall package was unfinished and broken mess. Gears of War 3 was was easily the most refined game in the series. Gears of War: Judgement was, for lack of a better word, unnecessary.
Uncharted has a bit of an uneven franchise. The original Uncharted was good, but unremarkable. Uncharted 2 on the other hand was a fantastic game, and one of the best games of 7th gen. Uncharted 3 was better than the first game, and even had the best multiplayer component in the series. But it took a nosedive in the writing department. It was obvious that Amy Hennig was barely involved in the development process. Then there's Uncharted: Golden Abyss, which I haven't played. Therefore, I can't judge it.
I enjoyed Uncharted 2 more than any of the Gears of War titles, but Gears of War has been more consistently good series. So, it's a tie for me.