It is very difficult to evaluate and compare two quarterbacks who only got a couple of series a piece. There isn't a whole lot I can say, but here are a few thoughts.
I thought Geno Smith generally did a pretty good job making his reads and delivering the ball. It also sensed he trusts Eric Decker. The big thing I wanted to see him do, however, was protect the ball. The play early in the game where he was pressured, his mechanics collapsed, and he threw a duck to the sideline bugged me a bit. That has pick six written all over it. I don't know how much you can really read into one play, but for the amount of time Geno played, one play like that is one too many. His first job is to avoid plays like that.
As far as Vick goes, his limited playing time makes him tricky to read. So does the fact he was guiding the first team offense against what appeared to be backups defensively for the Colts on the touchdown drive. One thing that really did jump out is that he still has some juice in his legs. Geno is a good runner, but Vick takes playmaking on the ground to another dimension. He added a little something extra in that way.
For what little it's worth, I think I'd give Vick a slight edge in his play, and I'm a bit less convinced I like how the Jets are handling the position by making Geno the starter unless he falls apart.
One thing I am confident in saying is I don't think Matt Simms should make the team. I see the exact same flaws. He has a million dollar arm, but his passes have no touch. He also doesn't have any idea what to do if his first read isn't wide open.