I'd love to raise river tiles to allow my units to pass along them quickly, but the engine doesn't allow it.

Actually, that's by design.  It was discussed at length - raise and lower land used to cost 50 mana, but then they were so prohibitively expensive no one could ever use them to say, make a pathway through a large mountain region.

Personally, I got accustomed to it and I like it.  It's not like you can abuse them too much, and it's a fun spell.

Not sure why being able to raise sea levels is unbalancing to the game?

It's also a 3rd level earth spell. So, it takes awhile to get access to raise land and lower land spells. Many of us beta users have already had this discussion with Frogboy when he lowered the spell cost. The point is usually we have to cast the spell 3-4 times before we can make practical use for the spell. I proposed 10 mana cost for each casting. They said they were not changing it and if we wanted something different we can mod it ourselves to be something else.

As to the floating waterfalls, the only way you are going to fix that problem is to change the floating waterfall definition.

Here is my fix of the problem. (Note: I've got nearly the same look as the original waterfall, but my talents lie in otherplaces besides artistry)

https://dl.dropbox.com/u/75549875/Fallen%20Enchantress/River_CliffEnd.xml

Basically move the other River_CliffEnd.xml file from your fallenenchantress\data\English\Core Tiles\Rivers\

and move this file in its spot. It basically looks the same, but it will avoid the floating waterfall problems. It's a temporary fix until the developers themselves decide to fix the floating waterfalls the way I did.