L.A.
We have the uppa vista and the citi mini Jogger (thank you very generous MIL). We also had a graco travel system.
the uppa has a bigger basket, and the seat adjusts more easily (one of four fixed positions). It is sturdier, and allegedly can even be driven on the beach. the main downside to the uppa is that it is really big and bulky. it gets stuck in supermarket aisles, and takes up the whole trunk if you mean to travel with it.
the citymini has the one hand fold which is really convenient. its got an ample sunshade, and is sturdy. its light and it drives well. on the down side, it has a strap and cinch mechanism for the seat adjustment (not so convenient). the foot rest isn't adjustable. there is no cupholder, or child tray included, and the basket won't hold much at all.
I stand 5'1" tall. Hubs is 5'11". the uppa can adjust up for taller people. (it doesn't adjust down enough to be comfortable for me). the city mini has a fixed handle.
The uppa has an arched brace accross the back. This is convenient because you don't kick your feet into that metal support that the mini has. the down side, you can't step on the bar to get some leverage to lift the front wheels up a curb, or over an uneven sidewalk.
one last factor to consider, is washability of the seat etc. I know that the uppa vista 2010 is not machine washable. I think the same is true for the mini. thankfully we haven't had any diaper blowouts or vomit incidents, but if we were to, I don't relish the thought of having to handwash either.
both are sound choices. If you are going to have only one or the other, think hard about your environment and usage. are you car people, are you big walkers, do you actually jog, will you be on subways and buses?
good luck and congrats to you.