I figured it's been a long time since I posted anything, so here it is.
This version contains a bunch of smaller bug fixes (including some crash-related ones) and also adds water physics. Samus will now slide around in water unless you get the Gravity Suit. In order to allow for backwards compatibility, this feature has been disabled in acid until I go back through all the levels and make sure the player can escape from the acid if he/she falls in.
The Zebes Depths area has been completed but has not been appended to the map quite yet. If you want to test it out, you'll have to set your SMTC.cfg to start you in Rooms/Dept00.mcl. I worked hard on those levels so at least pretend to appreciate them.
Scripting is in the works at the moment but is only partially functional. To see some examples of what it can do, go to your SMTC.cfg. The cvars on the bottom can be used to edit the properties of water physics in-game. More options will come once I work out the bugs in the parser.
As for the more global picture, Toasty and I have been talking about starting a new project. It won't be a remake, instead it will be a completely original game mixing RPG and Strategy elements. Very few details have been even discussed but you can expect to hear about any betas on this blog at some point.