I finished TW3 and am replaying for HoS, and I just finished Rise of Tomb Raider as well. So here's my personal opinion.
To be honest, I found RoTB massively entertaining. It was fun. Its story is definitely better than average. It's short, concise, with a memorable and believable villain, decent suspense, decent display of personal emotion and drama, and an acceptable ending. If we are only comparing "main quest line," as it is traditionally understood, then IMHO RoTB actually beats TW3. The extremely disappointing main villain alone in TW3 would've lost it.
The problem is, main quests are all there is for RoTB, whereas main quests are but a small and mediocre portion of the gigantic TW3. Other than finding Ciri, the remaining shiny spots in TW3 are all critical side quests: Bloody Baron, Keira Metz, HoS, Yennefer & Triss (and I really liked the Ice Giant) etc. And TW3 tied them altogether in a way no game has done. Adding onto that the choices and consequences, multiple outcomes, a good balance between humor/darkness/emotion and so on, there is no doubt for me that TW3 put far greater effort into story telling than RoTB. I mean, it is really hard to mess up a story like RoTB. Its small size, linear nature, and lack of choice-and-consequence make it practically immune to pacing problems. And it is short and focused enough that it can get away with only having one mood the whole time. Comparing the story of RoTB to TW3 is like comparing a single delicious main course to a seven-course meal with two bad ones and five good ones.
So if I have to guess, those guys at the Writers Guild don't really understand the uniqueness of story-telling in a video game, let alone an open-world video game. They didn't see the freedom, player choices, openness, diversity of mood etc. They saw a good villain, well-structured pacing, and they said "Bam, RoTB got it." But for someone who actually plays the game, TW3 is the king even if uncrowned.
Sorry CDPR didn't get the award. IMO losing this award shows more than anything else the risk undertaken by a true pioneer. CDPR transcended the limit of video game story-telling with TW3. They are the pioneer in creating open-world story-driven game, and they also paid for it. I have no doubt that if TW3 was as linear and confined as RoTB, CDPR would blow RoTB out of the water into oblivion with its story (just look at TW1 and 2!) TW3 story is far from perfect, but I have to give Kudos to CDPR for trying, and trying hard, to be the first in bringing in something new.