Hey, guys. So, I'm developing this Twilight Princess reimagining that's actually set in the Fallen Hero timeline. My problem is, where in the Fallen Hero timeline. I've narrowed it down to "sometime after A Link Between Worlds" and "Sometime after Zelda II." Which do you guys suggest?

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Well, unless you're planning on coming up with a completely new villain, after Zelda II won't work since Ganon is dead forever. So I would suggest after LttP/LbW.

You could bring a bad guy from earlier in the timeline.
Maybe?

Why does Vaati not appear again in the Fallen Hero timeline?

I'd recommend setting it a few years after Zelda 2, to make it a Trilogy.

For the villain: Demise's Hatred doesn't have to be Ganon/Ganondorf. Perhaps that hatred would transfer to the Zant of this timeline, giving him the power he needs to Usurp directly.
Or it could be a villain from before the Timeline split. Vaati or Ghirahim could fit this role nicely. (You could even use the idea that the latter would be trying to bring back his Master directly; not the "incarnation of Demise's Rage", but full-on Demise himself.)

Also, a thought I had:
Would Original Link even turn into a Wolf?
ALttP Link turned into a rabbit, while Twilight Link turned into a Wolf. Sure, it's probably a different transformation, but you could do an argument for personality. (Noble protector with a fierce side vs something that only looks unassuming, but is very fierce and so often underestimated.)
Wolf Form seems bound to the Hero of Time's descendants, so it might be good to use another animal that fits thematically.
Ultimately, though, it's up to you.

Another thought worth considering: if you go with the Hero's Shade, it might be best to not have it be Link. Rather, it might be fun to have it be OoT!Zelda instead. That would open more story possibilities.
(She could teach you both magic and sword skills, the latter being Dark-Souls style parrying/Riposting and unique Battle Mage skills. Her form could be a magnificent golden hawk.)

Hope this isn't too long or rambly. I've thought about this myself, and wanted to share my own thoughts with you.