Will it be possible to gain a neutral or positive reputation with alien races that are hostile to the UEE?asked by Zindo

Absolutely. The Vanduul aren't cuddly. But if you're going to go off there trading with the Banu or the Xi'an, the UEE may not like it sometimes, but you can do that.

So you can up your reputation with the other alien races by dealing with them?

At least some of them.