I suppose they didn't want to waste them. Maybe they thought the Syreens would change their minds about being slave shielded. Maybe they wanted to find out if there was any tech in the ships they could use. Heck, maybe it's just there to make you do side quests.
Well there is probably a cache of Earth Ships floating around somewhere as well (as well as Chenjesu and Mmmhrm (sp) ships... its just not worth getting them as you can build as many ships as you have pilots... The Syreen wanted their's immediately- instead of retooling their starbase, remember you transferred a fair chunk of your barge onto the Earth Base.
The Syreen surrendered with much of their fleet intact (but very badly equipped), while Star Control seems to have thrown every single Cruiser available at the Ur-Quan in a last-ditch attempt to slow them down.
In other words, the Syreen are probably the only Alliance member with ships in storage, as they were the only "fallow" slaves that surrendered with a large amount of ships left.
Besides, their whole reason to fight were pretty much gone. They only joined the alliance because they didn't had a home planet, a big part of their fleet wasn't capable of hyperspace travel (I don't remember how much, but over half I guess), were basically a sitting duck in alliance space and one of the races fighting on the Ur-Quan side were the VUX who had been preying on them for generations. I bet they did planned on fighting till the last woman before they knew of the Ur-Quan's idea of how to threat those you've defeated. (has anyone ever seen a male Syreen, they are pretty rare). But after the Arilou abandoned them (Humans safe, who cares about those blue hypnotizing freaks), they grabbed the Ur-Quan's offer for a new homeplanet with both hands. Of course the red slaveshield ruins the view a bit, but hey, it is better than being blown to pieces, right? At least until the Kohr-Ah come and pay a visit.
And the Ur-Quan probably have something against wasting resources.
Logged
,,That was the worst and most boring movie I’ve ever seen. Lousy special effects.” Sergeant ironhead. The real reason why the alien brain on Cydonia was destroyed while in the middle of displaying a message telling the X-com operatives not to fire.