As a Wiimote+Nunchuk veteran I've sworn by separate Joy-Cons since day one, especially because the attached handheld mode turned out to be an ergonomic disappointment, and after the Wii and Wii U eras I'm not even that accustomed anymore to holding my hands as close together as the included grip demands. In handheld mode I was cramping up in no time at all, while with detached Joy-Cons I was putting ten-hour days into BotW without breaking a sweat. Freehand aiming and a more palpable sensation of HD Rumble were a bonus, made clearest by the Splatoon Testfire.
However, I did have one overriding concern about this control scheme, and playing the Blaster Master Zero demo this weekend confirmed my fears. The pseudo-D-pad buttons aren't well placed for a separate left Joy-Con to be good for intense, precision-demanding D-pad-based games like a future 2D Mario or older VC titles, once they show up. The only way to play comfortably with the directonal buttons rather than the stick as the main input is to hold the left Joy-Con much lower, losing easy access to ZL/L and also losing the advantage of having the bottom of the Joy-Con rest against your palm, one of the things that make the detached setup feel surprisingly stable. (I don't have that problem with Puyo Puyo Tetris, oddly enough.)
I don't know if those of you playing Shovel Knight with separate Joy-Cons have had a better experience with this, but for me this is enough of a concern that it's yet another reason for me to hold off on double-dipping and play all the new content on the Wii U instead.
Attached handheld mode isn't too bad with D-pad games as opposed to stick games, at least, as the placement encourages a looser grip on the device. It's not wonderful, but it's not unlike playing on the 3DS. So when a 2D Mario or the VC library comes around I do see myself using the attached mode or the bundled grip a lot more than I do now. For everything else, howeverparticularly anything involving stick movement, motion aiming, or the rumbleseparate Joy-Cons are clearly the way to go.
I am definitely in the market for a future Joy-Con (L) that has a classic Nintendo D-pad in the top position where the analogue stick currently resides.