For me personally, there is usually one box legendary that has a much better design than the other and therefore it makes which version I buy quite easy. If I just ignore the 3rd version legendaries for now, my choices have went Groudon > Kyogre, Dialga > Palkia, Reshiram > Zekrom, Xerneas > Yveltal. My exception to the rule was always Lugia & Ho-oh because they're both great, though I prefer Ho-oh.
In this case, I'm not a fan of either design, but at the same time, neither of them are terrible. I would probably place them both above Kyogre and Palkia, both of which I find very ugly, but below all the others. I also prefer all the 3rd version mascots over these two (Zygarde would be the exception to this in a parallel universe were Pokemon Z exists). Regardless of the potential third mascot, I would say this is easily the worst concept for the duos/trios so far.
Solgaleo probably narrowly beats out Lunala for me, but I've pre-ordered Moon version which is probably the first time the cover mascot hasn't made the decision for me.
If I was going to order this by generation then it would be as follow. This should also be considered a tl;dr because I realise no one should post this much about the quality of cover mascots.
1. Ho-oh / Lugia
2. Xerneas / Yveltal
3. Reshiram / Zekrom
4. Solgaleo / Lunala
5. Groudon / Kyogre
6. Dialga / Palkia