I think "water elevators" are such an ingrained and practical feature in MC that you'd face a lot of opposition if you tried to take them out. I agree with you they might make spelunking a bit too easy, but considering it isn't hard to build a stone pillar under yourself or dig downwards to get where you want to get anyway, I don't consider it much of a problem. Keeping water elevators in gives us the option not to use them if we want to play an "immersive" game.
Water physics (like in the Finite Liquid mod) drain too many system resources to be feasible, unfortunately.
If somehow water that is falling detects a object in it's path it would be cool if it could instead of moving around that object to the front, detect in there is water on it's sides, then just continue it's flow as part of the side falls. Adding to the effect of the liveliness of the water when it hits an object like a rock or another body of water, it should have a cloud hanging in the area around it.
Furthermore, water that is not falling but still moving should appear more rough, or have white bubbles in it to simulate rapids. The only three times water ever moves is in the ocean over holes, when the world generates a fall, or when a player is playing with a bucket.
I agree to a point. It would make it alittle harder to travel the waters though, so I would keep where most water is at "sea level" like rivers that separate biomes, oceans and swamps. I would love to see this in jungles by having rapids that leads to a fall. Awesome idea.
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"If it already has been done then it can be done again" or
"If its a mod its possible to be a feature"