While Metroid Prime 3 is amazingly beautiful it doesn't stand up technically to the conduit. 
See More Metroid Prime 3: Corruption Screenshot at IGN.com
See More The Conduit Screenshot at IGN.com
I have to give credit to prime 3 for the nice lighting, and less aliasing, but in everything else the conduit is superior. Textures are more detailed, there are more polygons, some character models such as your main character are more detailedin the conduit, but overall Metroid Prime 3 has better character models. The gun models are more detailed in the conduit though compared to samus' cannon. I will give metroid prime 3 credit though with the better art direction and is by far the better looking of the two, but the conduit overall is probably more taxing on the hardware, and you notice it by seeing the game run at 30fps while prime 3 runs at 60fps. Now you might say it's because retro is more familiar with the hardware than high voltage. Both of these games are inferior to games like Fatal Frame IV or SMG though in the graphics area. I could see the next Zelda besting all games on the wii though.
Edit: If you haven't noticed already I'm a big metroid fan and beaten corruption 7 times.
