Really? If anything, I honestly believe that Doom 3 has aged a lot better than Half-Life 2 in terms of gameplay. Half-Life 2's greatest gift to the FPS genre has been physics puzzles, which, while innovative in 2004, are just not very interesting or creative 10+ years on. Doom 3's gameplay is relatively simplistic in comparison, but that's also arguably it's strength - the more fast-paced, action orientated play style still feels good, and indeed, downright unique compared to any other modern game.
Can't say I fully agree with your assessment of the two.
Half-Life 2 was about far more than physics puzzles. The two biggest things that the Half-Life series did for shooters was the incredible pacing and storytelling through gameplay. Pacing wise I don't think many shooters have touched Half-Life 2 to this day.
That game constantly has you doing something new almost every step of the way, the physics stuff was just one part of that. You also had vehicle sections and even a couple of times where you fight alongside others. And their way of telling story was incredibly influential as well.
Doom 3 on the other hand was the first time I remember really feeling like a game had atmosphere, which was really due to it's implementation of a unified lighting and shadow system. That was the most realistic damn thing we had ever had up to that point. And the gameplay was incredibly tight and exactly what you expect from an Id game.
I think both games hold up incredibly well in their own way, though enough cannot be said about how forward thinking the tech in Doom 3 was.
Both of these games dragged like hell toward the end though. My biggest gripe with Doom 3 is that the game does very little to break up the monotony of killing the same mindless Imps walking down the same kinds of dark corridors for 10-12 hours. Thankfully the gunplay was great but the small, samey levels didn't exactly lend themselves to much variety. Half-Life wins there.
2004 was such a great year for PC shooters. Far Cry, Doom 3, and HL2 all in the same year, all pushing technological boundaries in different ways a year before the next generation started.
