Just because there aren't as many known exploits for MT doesn't mean it's more secure than WP. That's the same argument used when people say Apple software is more secure than Microsoft software. Yet if Apple software was used by more than 90%+ of businesses, it's likely more people would attempt to (and possibly find ways to) hack it.

Security aside, MT has lots of issues -- performance (or lack thereof) being one of them and bad upgrades being another. After the third time an upgrade broke some sites I manage, I gave up and migrated some sites to WordPress and some to Drupal. Have yet to come across the same issue.

MT does not disclose many security issues and instead slips fixes quietly into new releases.

It also seems to have not as many users.