Hello Sam,
So lets get the obvious stuff out the way.
From/To Pump is implemented and is the new default in the mod since 0.5.7. Able to be toggled!
Water Regen is also already implemented, from version 0.5.6. Able to be toggled!
I always liked the idea that this huge body of water that was in the middle of the base is now land accessible, instead of having to use landfill to get rid of it. To counter this I have thought about adding in, being able to dig (landfil) shallow/deep channels that you could fill with water. Allowing you to make your own moats for defense. Though this would be tricky to implement at a mod logic area, depending on previous areas and merging them.
As for the boundaries with cliffs something to think about, though if i go with the channel digging idea would make this no longer required.
Either way at this point, apart from one further bug to release a fix for I'll wait till after 0.17's release before making big changes. I'll keep this in mind.