They're both great games and I liked them both. I did feel that the main plot of Witcher 3 was more interesting because it was more personal.
In Inquisition I chose not to engage in the "faith" aspect of the story. I was sceptical about being the Herald, and about Andraste's divinity in general. That was fine and I enjoyed it, but it also meant that whenever any character went on about the Maker and destiny and the Chantry being this important institution I was uninterested and disengaged. I was a little disappointed that no matter what actions I took in game, my PC was regarded as a religious icon and the Inquisition as a religious organisation. I'm just here to save the world, not solve your metaphysical crisis.
The Witcher 3 was a familiar story about family and one man against the world. Seeing Geralt get emotional about/with Ciri was great. I loved even potenially antagonistic characters like Djikstra and Philipa, and the relationship between Geralt and Ciri, Yennefer, etc. At the same time it's a little weird with world building and lore. I'm not that well versed on the Witcher setting, but I know Geralt fought in at least one war against Nilgaard, and yet working with them and possibly securing their victory over the Nordlings is dealt with without mentioning that. And if you played through Iorveth's path in TW2 and were expecting to see the impacts of that in TW3, sorry but not happening.
So I liked the main plot of TW3 better because the story of one man fighting for his family resonated with me more than Inquisition's story about a reluctant prophet, but thought Inquisition was better with world building and respecting previous entries in the franchise.