Personally, what I did with amphibious was have it allow units to swim through coastal tiles at reduced stats (-2/-1 while swimming, might actually increase that to -3/-1). IMO this makes it a vastly more useful promotion, surprisingly helpful to units that will make use of it (recon units especially benefit greatly), while still not making it a "must have" promotion, since units that do inland combat won't get much use out of it, other than the rivers bonus. The stat reduction is mostly to keep Drowns useful, and to keep Amphibious units from being able to fight boats effectively. Oh, and for obvious balance reasons I made it no longer available to Mounted units.
This is probably unbalanced and not good for the main game (reducing it to only require Combat 1 might be a better idea for the main game), but I find it fun.