Well the only thing that I can really recommend is looking at these tutorials;
The Mapper's Tutorial and
No1's Tutorial. Start using full raw instead of mixing autoborder. And yes, I mean even do mountains with raw.
So you will have a result such as this
Instead of this
You should also add onto your doodads so they only have these
Instead of these
If you need to know how to create a new palette look
here.