Initial impressions are pretty good. I've played for a little over two hours of Black Flag, mostly going straight for story missions (for anyone new to Black Flag - it really limits what you can do at the start of the game, so it's best not to get distracted by the open world stuff and progress through the story, at least until the point where you can freely sail). I've played 100% handheld so far.
In handheld, framerate looks steady and resolution looks to be native. There are quite obvious jaggies, but those edges are clean enough to suggest it's 720p handheld all or almost all of the time. Black Flag is a game packed with detail and that mostly translates well to the Switch screen, but things like leaves on mid-distance trees will shimmer, and the lighting model doesn't extend to the horizon (lighting looks fine on the ground, but higher up that can cause some far-off objects to look strange). Sometimes NPCs dither into existence as well, which looks a bit odd. These are all minor things, the kind of compromise that AC games almost always have to make, and they don't harm the game.
I have noticed one strange graphical glitch which has happened on several occasions when turning the camera, and looks like a vertical screen tear (as in, a tear dividing the screen vertically, not horizontally). Whatever it is, it's not actually screen tear, but I can't describe it any other way. It lasts for a split second and then it's gone, but it is noticeable for that split second.
Gameplay seems entirely unchanged which is mostly a good thing. Several things about the way AC games worked back then will annoy newcomers and anyone who's only played Origins and/or Odyssey - tailing missions are irritating and chasing shanties is just an awful way to obtain them - but the game still offers tons of freedom, a great world, and plenty of stuff to do.
I still have a long way to go but provisionally this is the best handheld Assassin's Creed purchase ever. The competition isn't exactly fierce (Bloodlines, Liberation, the DS games, Chronicles, ACIII, Liberation again), but a good AC game getting a good conversion to handheld has been a long time coming.