Problem is that every tile onscreen will be "synchronized", i.e. in one phase. It's only the smoke which has phase randomized. To make them look a bit diversed, you'll have to make extra MCDs with another "phases", but that will lead to altering maps too.
In UFOEU only arctic tileset has terrain animation (water). TFTD has more animated things, but sometimes it feels even overly.
But really, i would like to invent "random phased" bit in the MCD, to avoid map rebuilding, and in the same time provide visual "evenness" of terrain animation.
For example, byte38, is always 3. For no reason. Unused byte in the MCD. We can use it. If byte38==0 and MCD is animated - init tile with random phase (0..7).