Some kneejerks:
* Paladins / Great Knights tend to always have weapon triangle disadvantage and thus lose horribly.
* Falco/Dracoknights with swords have the same problem (Palla, Caeda).
* Lords tend to have busted stats in their home game, which is less true in an all-star cast.
* Mages (barring Sanaki) can't really change their weapon triangle identity in-game, so I'd be skeptical of them doing so against the Heroes cast by equipping a different tome, buuut if you let them get away with this, it's trouble for Heroes. For all that it hardly matters since Heroes can't counter at range 1, a pretty crucial weakness in a DL duel.
* Swordmasters tend to be super-dodgy in their home games, another thing that doesn't translate... although you can argue that their Heroes counterpart would have super-skill or something, I guess. Kind of a problem for FEH swordmasters.
* Most FE Manaketes traditionally have fantastic resistance (even when they don't in FEHeroes - see Adult Tiki), so most of the Heroes manaketes are getting bodied.
* Healers in Heroes have damage that is just too terrible to win, ever.
* Dancers tend to have utterly garbage stats in their home game - Olivia / Ninian, maybe Azura too. So hey, there's a win for Heroes.
Archers:
SetsunaH should win, thanks to Bowbreaker?
VirionH stands a shot as well; I think Sniper Virion needs 5 hits to kill, and Brave Bow is ticking up the Astra counter faster, so VirionH resolves Astra and wins. Dies horribly vs. Bow Knight Virion13 of course, who has Bowbreaker.
Axe users:
BartreH is really tough on defense, so might just outtank Bartre6/7 despite the Fury self-damage. Even has Desperation hax.
HawkeyeH might win too just because Hawkeye7 is kinda garbage.
Anna gets wrecked by Anna13 (weapon triangle disadvantage), but might beat Anna14 (hits the right defense, 14 hits the wrong one) despite counter woes vs. Shining Bow.
Other stuff:
SelenaH might win thanks to THREATEN SPEED hype, which should allow her to double? Evasion / Sol gives her problems ANYWAY, which is kinda sad, but it's a good fight.
MatthewH has a shot if you just totally ignore evasion? This is true of a few others I guess, too, but seems a notable case that's a bit more clear-cut.
