(This should be issue type Improvement, but the drop-list just said "No Matches" when I tried to change it. That may be on my end, my connection's pretty bad.)

Water has two major flaws as currently coded. It would be nice if future versions could remedy them.

The first is that water displays the flowing-down animation in the sides when it encounters any transparent block, even if it's illogical. It's hard to see a way around this for some blocks, but not for others. For instance, it displays this animation against glass blocks, which logically ought to provide an unobstructed view through them, as in the case of aquaria or submarine windows. Conversely, the animation should not play against the backsides of stairs or the topsides of top-half slabs, since those sides are not transparent. This is more transparency's fault than water's, but it may be possible to change water's code to compensate.

The second is that water flows into any block with material water and metadata greater than 0. ANY block, not just block 008. It doesn't currently affect anything in vanilla Minecraft, but it makes mods featuring underwater non-solid blocks such as coral very difficult to implement, since any of these that use metadata will generate "vortices" of inward flow in adjacent water blocks.