Alright, I will try to be as unbiased as I can be. These are purely my own opinions and I recognize others may differ. So here goes
1) Technology-wise goes to Mission:Space for creating a one of a kind ride system that produces experiences not felt on ANY other ride. On the surface some may say it "just spins you" and that is the magic behind this. It is SO well-done that only when you take a step back and think about it that the complexity of the ride system really comes through. Spiderman does an amazing job of blending technologies already developed (3D films and motion-based forward moving ride vehicles) into a great attraction, but does little to push that technology boundary than had been done prior.
2) Thrill Wise: Again to Mission:Space. Spiderman is a lot of fun, but it never got my heart pumping like MS did, especially leading up to the actual ride and then lift-off. Spiderman has that cool "falling" scene, but it doesn't get my adrenaline pumping like MS did.
3) All time experience wise: This one is tough. MS produces an experience that is truly "out of this world" and provides a fun way to educate people on astronaut training and spaceflight with out being "preachy". You really do come out of it at the end with a feeling of "accomplishment" almost, if you know what I mean. Spiderman on the other hand is just a lot of fun with some great effects and laughter. It produces some great motion-based movements to a often spectacular 3D film. I would say I came off Spiderman smiling more than when coming off MS, but if I had to tell someone which one to definitely experience it would probably be MS for its one-of-a-kind sensations and the reality the entire attraction is based upon. However, Spiderman may be more "fun".
4) Well themed and exciting: Exciting once again goes to MS, hands down. As I've said before, the way launch gets your adrenaline pumping is something Spiderman doesn't do at all. As for themeing, the winner is split. As for the queue (not including outside decor), the winner is Spiderman. There are numerous things to look at in several rooms, including the cubicle-room that I find helps push the queue over MS's. As for actual ride themeing, I would have to go with Mission:Space. Spiderman often drops the ball here. When you aren't directed in front of a 3D screen you know very well you are inside a warehouse and not the streets of the city. The blue coupe you go in also brings the ride's themeing down. Their is no creativeness to the look of the vehicle's outside. Had it looked more like a "car" or something else, I think it would make more sense. Considering MS is a training facility, the outside of the ride vehicles don't matter. What does is that when the pod doors are closed and the control panel moves forward, you REALLY feel like you are inside a space shuttle. The blinking lights, monitors, sound buttons, switches, joysticks, etc. It is truly realistic.
So what is my choice for best attraction overall? You probably guessed it already. My choice for the winner is Mission:Space. I really tried to take a step back and think about it and overall I think MS, with its preshows, ride, great postshow and sense of reality, really pushes the overall experience to the next level.