We in MSSA have chosen not to utilize the AT to manage subject terms for three reasons.
First and foremost, subject handling in the AT is not as robust or or as functional as our current cataloging system.
Second, only a portion of the finding aids we imported contained controlled access points. This is because subjects have generally only been assigned to our master collection records, which are our MARC records. Only for a short period of time were controlled access points used on the manuscripts side. Furthermore, given the differences in content and purpose of MARC and EAD, trying to consolidate the two into a single system presented obvious practical issues. So, rather than try to programatically marry our MARC subjects to our finding aids, we decided to maintain access points in MARC until the AT could serve as our master record--a scenario still some ways off though made much simpler with the introduction of plugin functionality and custom import/export tools. In fact, with plugin functionality we might revisit the possibility of at least importing our subjects from MARC and attaching them to our resource records in the AT.
The third reason we chose not to use the AT to manage subjects was the difficulties the AT has roundtripping data, especially from one format to another, and the concomitant need therefore to develop tools to clean up this data for easy import into Voyager.