I try not get hung up on the “main” and “off” labels, especially because I don’t think Mercy fits either of them very well. I see her as more of a flex support and I think she’s the only one who really functions that way. But yeah, a lack of a purely-defensive ult like Lucio’s or Zen’s is what keeps her from being a great pick in popular “main + off” comps. I wouldn’t call it a harsh tradeoff, though, because of how generally flexible she is throughout any given match.
While Valkyrie can’t counter burst damage, it has the benefit of being useable in almost any other situation to give your team a fifteen-second edge. It’s much more flexible. You can’t use Transcendence or Sound Barrier nearly that freely because then the enemy will know you’re open to ult combos. Valk also charges more quickly than those ults so you can use it early game for an early edge.
It’s just important to know when Mercy is a better pick than someone with more utility. I use her primarily when my DPS stand to really benefit from damage boost and in spread-out comps (where you don’t really need defensive ults and GA can take full effect). I try to stay away from her in grouped-up, ground based comps or when paired with a low-HPS-output support and tanks with low self-sustain. If I’m going to have to pocket the tanks for any reason, Mercy isn’t the right pick.