Here it is, fashionably late to TA's 16th birthday, the one you've all been waiting for: the Total Annihilation v3.9.02 Beta Patch featuring the all-new, fully-interactive megamap as well as fixing almost all issues with the previous version and adding numerous new features.
UPDATE: To anyone who can't launch their game due to a crash or DirectX error, please see this post for a preliminary hotfix.