I recently obtained a Fleet Aquarius Escort. Here are the problems I ran across with it thus far:
1. When customizing the Aquarius Destroyer, it only shows the Type 1, 2, 3, 4 and Fleet materials. The Type 6 and Veteran materials (the former which is available on the 'normal' Destroyer, and the latter due to the Veteran rewards I am entitled to) are missing.
2. When trying to assign science bridge officers to the Fleet Aquarius Destroyer's universal stations, the UI is unresponsive. I have to set a bridge officer of a different profession, and then switch to the science Boff I wanted for it to work.
3. Many dialogues, both in space and ground environment, refers to my default ship's (the Fleet Aquarius Destroyer) as that of my default shuttle's instead. Furthermore, any bridge officer dialogue will be based on the bridge officers slotted in the default shuttle, rather than the default ship.
i.e.: default ship "Sacagewea" (a Fleet Aquarius Destroyer) has 'science bob' and the default shuttle "Sunset" (A Delta Class Shuttle) has 'science billy'. I am playing as the default ship. Say I encounter a scenario that has a NPC address my ship by name, it will call it "Sunset". If a Science boff character is to report something showing on sensors, it will be 'science billy' speaking.