Mostly it has to do with Valka - specifically her effect on the first movie's canon, and on the importance of what Hiccup did.
Firstly, Valka does not exist in the first movie. Hiccup's mother was literally a different person at that point - Vallhallarama, a warrior-woman, hinted at in the film and previously a living character in early drafts. There are sketches of her in the artbook, and surely is what the writers had in mind. I'm pretty sure it wasn't meant to have a sequel at that point.
So, swapping out Valla for Valka messes with canon - most glaringly with the "breastplate hat" joke, but also in so many small ways. Comments should be made alluding to Valka's fate ("making friends with dragons? Your mother tried, and she got eaten by one!"). Stoick should have at least mentioned her when he's talking with Gobber early in the film. Things just don't sit quite right.
But ultimately, Valka's backstory undermines the significance of Hiccup's actions in rejecting the war against the dragons. He's no longer "the first Viking in seven generations who wouldn't kill a dragon", he's "son of Valka, who did it first".
It's all rather unfortunate. I like Valka. I like seeing her and Stoick and Hiccup as a family (though it's also jarring when I think about it because I've had Valla in mind up until now). I just wish it had played out differently.