One I know bugged me about 3e, is that an elephant falling off a cliff will much more likely to survive it than a mouse falling off of a cliff, and that is not how the square-cube law works. I houseruled that in my home games many years back now (fall famage is the same for medium creatures, but for each size below the damage is halved (down to 1) and then the increment is doubled from there; while for creatures above medium, the increment is halved to 5ft, and then the damage doubled per increment beyond that (and naturally flying creatures count as... IIRC 2 sizes smaller for fall damage).
