I always considered Vera to simply be someone who was taught magic, possibly by Dalton considering her high ranking in Porre. Afterall, Radical Dreamers also shows us that nobodies such as Serge can be taught magic by someone with the know-how (e.g. Magil).
She could be Marle, but that throws up so many questions, such as "Why is she so old?", "Why is she working for Porre?", "Where's Crono?", that I prefer to go with the Occam's razor route.
Vera being Queen Zeal makes no sense, personally. There's no reason to bring her back. Then again, there was probably no reason to bring Dalton back either...
Also, maggiekarp! Welcome back!