Sure there is a reason to use them. Some people fall in love with low tier ships and want to pilot them at T5. Not everyone is a minmaxer and prefer style over power so piloting a T5 Nova is preferable to a Deep Space Science Vessel.
Proteus, you can ask the same thing to the Jem'Hadar bugship and the B'rel Bird of Prey - both of which are Tier 5 ships; the Aquarius is actually in a similar size category to them. Pipsqueaks, you say? I call them "little dudes with attitude"!
The ship was asked for, and now it's in. Now, the point is to help make it as rewarding to use as most other player ship. Let's stick to that, m'okay?
Speaking of 'shuttles', one feature I was really hoping the Aquarius destroyer might have is the ability to be swapped to from an Odyssey bridge's transporter room like we can with the small crafts. That way, no need to return to a starbase to swap the ship back and forth. Want a DPS role in an STF? Grab your Aquarius! Your team needs some extra staying power for that freighter defense mission? Switch back to your Odyssey!
It's just utility, but it'd be awesome. It's one of the reasons I was hoping the Aquarius would become playable.
Great idea, it would also be cool if you could control and give it orders ( the escort I mean). Or, you could pilot the escort yourself( and the Odyssey,along with all of your abilities and weapons; would become NPC!