On the otherhand, Yuri and Estelle are often the two characters chosen to represent Tales of Vesperia and make the most sense as Representatives of Vesperia as a whole. Just because you think Yuri/Flynn would be better and have reasons behind it doesn't mean they follow your train of thought.
Frankly, I definitely prefer the synergy of a team that mixes Swordplay and Magic. Using Estelle leads to "one less person with a sword", leading to more unique combo opportunities. Its bad enough we have Ryu AND Ken in the same team, leading to basically lots of back to back Shoryuken combos.
To show a parallel...
Frank West/Hsien-ko I mentioned above. Why is Hsien-ko Frank's partner when he has an obvious Partner in Chuck Greene? Makes sense to have the two Dead Rising protagonists together, especially since they worked together canonically in Case West. Yet it seems they opted for Hsien-ko, who has no relation to Frank West whatsoever other than possibly wishing to reuse the NxC joke of "Hsien-ko + Zombie Killer" (only this time, its Dead Rising, not Resident Evil.)
Or Dante/Demitri. Why not put Dante with Trish, his actual canon partner in the DMC series? THe best reason I can think of is for a funny sitcom duo between the two, given their Personalities would clash, and I can only imagine us getting introduced to both with them beating the snot out of each other, with neither getting in any sort of advantage then "Oh crap, LOTS OF MONSTERS! ...truce?" scenario.
They obviously want to do some unique team combos for interesting team synergy. Just because Flynn gets buffed when Yuri gets buffed and what not doesn't mean Flynn will actually lead to an interesting duo. Rather than just going "WHY DID THEY DO THIS!?", try to consider the kind of things they were taking into account. Having an open mind in these things is nice.