A bit of an oddball that I found when looking around about the Memory Link feature in BW2, but one oddity I find is the Cheren Memory Link battle.
It seems pretty unsurprising that most of his team is the post-game team he had in BW1. But there's one difference: he uses a different elemental monkey.
In BW1, naturally, Cheren had the monkey corresponding to the one that would cover the starter he chose. If you chose Snivy in the linked BW1 file, he'd have Emboar as his starter, making Simisage his monkey. If you chose Tepig, he would have Samurott as his starter, in turn making Simisear his monkey. And if you chose Oshawott, then he'd have Serperior as his starter, and he'd have Simipour as his monkey.
But in BW2, the monkey he has is different. He still has Emboar as his starter if the BW1 file you linked has Snivy, but instead of Simisage, he has Simipour. If you chose Tepig, his BW2 battle instead has Simisage instead of Simisear. And if you chose Oshawott, instead of the expected Simipour, he instead has Simisear on his team.
There is a trend there, however, but it's odd: the monkey Cheren uses in his Memory Link Battle in BW2 is not the one he had, but the one you likely had. If you link a Snivy file, then he has a Simipour, which you as the player likely had in that file, since THAT was the monkey you were given in the Dreamyard to cover Snivy. And vice versa goes for Tepig.
Still I find it strange: why would Cheren not have the monkey he used, but instead the one you, the player (aka Hilbert or Hilda) had. It's a bit odd to me, and I wonder why they have Cheren use *your* monkey and not his.
That also raises the question: if that's not his monkey, is that supposed to be the monkey that Hilbert/Hilda originally had? And if so, why does he even have Hilbert/Hilda's monkey in the first place? It's pretty odd. Bianca does not change the monkey she uses in her Memory Link battle, which makes this an oddball and raises some questions.
On an unrelated note, this also raises the question of the absence of the Forces of Nature in BW2. Unlike the Swords of Justice, Tornadus, Thundurus, and Landorus are completely unobtainable in BW2. Perhaps this means that Hilbert/Hilda canonically captured them during their adventure in BW1? I do wonder why they don't show up at all in BW2 and have to be traded over to be used in BW2.
These are two big mysteries I find with BW2, and raises some questions about things that happened in the interim between BW1 and BW2, and whatnot. But especially the first one: Cheren in his BW2 Memory Link Battle having the monkey corresponding to what you would have in the linked BW1 playthrough, and not the one he had, is quite a mystery to me.