I think that Xerneas is certainly going to be a top tier threat, I think the reliance on Power Herb to sweep its going to be it's Achilles heel. Towards the end of gen 5, Roar started becoming rather popular among top players, and with Xerneas being around, I expect that trend to continue. So against stall teams, Xerneas might have less set up opportunities than you'd think! Also, depending on how much of a boost Assault Vest is, you may have some stuff like Metagross giving it problems. It's still going to be an EXTREMELY dangerous sweeper that will probably change Ubers team building, but currently, I don't expect it to be unstoppable either.
Roar never became more popular; it's always been a reliable phasing move for a few Ubers Pokémon, no more, no less. I don't see how Roar became any more popular toward the latter part of Gen 5. In fact, I would actually argue that Roar lost popularity due to offensive's superiority in BW2 (moreso than BW1; stall was quite viable) in many regards. This faulty statement also makes your point of Xerneas being easily phazed quite the contrary. If you think about the common Roar users, Giratina-O, Kyogre, Groudon, and Dialga come to mind as the best users of said move. Other common phazers including Lugia, Ho-Oh, Skarmory, and co. are all OHKO'd by Xerneas at +2 after Stealth Rock. Due to the weather nerf, the two best spinners in the tier, Kabutops and Excadrill, suddenly lost a lot of viability which makes Ubers, a tier notorious for impossible spinning, even harder to spin in. Ho-Oh and Lugia are not going to be at 100% in any normal battle conditions to check Xerneas, and Skarmory most certainly isn't going to have its Sturdy intact to Whirlwind the fairy out. This applies to Forretress utilizing Gyro Ball as well. Donkey and I have experimented with stall, and needless to say, it is quite hard to make. Xerneas itself is quite a thorn in stall's side coupled with the other behemoths such at Specs Kyogre, so our best build had to condense our teamslots greatly through the use of Specially Defensive Aegislash as the spinblocker and Stealth Rock Gliscor among other Pokémon with relatively high opportunity costs which led the build much to be desired, even with the best of ideas coming together for the team. Metagross is a very unviable Pokémon; I do not see how you can argue it even has a niche in Ubers except being a specialized counter to Xerneas and an inferior check to
Lati@s compared to other, better Pokémon. Scizor is interesting, but the lack of Roost and Toxic for Arceus-Ghost is a set off. In a Xerneas vs stall situation, if the stall team is lacking a healthy Specially Defensive Kyogre, Substitute + Geomancy Xerneas can set up a second Geomancy on Chansey with 101 HP Subs (it's only like 44 EV's in HP) and it's practically gg right there. Xerneas is quite the threat, and I do believe that some of your arguments are not quite valid in your post. I do agree with your on one thing, however, which is that Xerneas will indeed change teambuilding.