Looks beautiful, but sounds like you caused yourselves a lot of pain. Obviously I don't know the details of your game but I would have put the orthogonal camera at a 45 degree angle so your environment could be a genuinely flat floor with upright trees/buildings/units (and scaling to compensate for sprites angled at 45 degrees). Then gravity/physics would work as expected, sorting/batching would work as expected, 3D trajectories and LOS would work as expected...
That said, I'm working on my first Unity game after decades on a proprietary engine, and it certainly can be hard to find just the right bit of critical info. Thanks for sharing your experience!
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qixotl - - 1 comments @ Why you might wanna think twice before making an old school-like isometric strategy game in Unity
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qixotl
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Co-founder of @QuantumSoupLtd and @GamesWales North, formerly at @TTGames & @EA • #Gamedev speaker • @BAFTA member • Roleplayer, atheist, goth, proud dad