At the end of the day, physical access is king.
Even if Mikrotik used a hashing algorithm instead of the encoding they have now, brute force attacks could be used.
If they removed the backup-before-reset feature, then the attackers would just PXEboot into a linux distro and mount the flash directly
(See
http://manio.skyboo.net/mikrotik/)
If people are breaking into your safe to steal the gold, there are only 2 real solutions:
1) Make the safe bigger:
Better locks / security, tamper tags, detection and response when the device goes offline. Either record or catch them in the act and have them prosecuted.
2) Take the gold out of the safe:
I know it makes management more difficult, but the real problem you have is that if you get one password, you get all of them. Stop reusing local passwords. Set the local admin password to something random and unique to the site, then enable centralized password management (RADIUS) for the rest of the user accounts.
This isn't an issue Mikrotik can really solve. All routers have similar problems and vulnerabilities, some are just more widely known than others. Start with the migration to RADIUS and you should see great improvement (plus it makes logging and managing user account access a great deal easier). Good Luck.