Well, yeah. I'm thinking of getting into Code Lyoko and I don't know which episode to start with. I've seen parts of both and I'm not sure which one I like more (maybe the prequel), and I'm not sure if I should even make the decision based on that. Halp?
Welcome to the forums! It's good to see some new life here.
I think it depends on whether you want to dip your feet into the lore of CL first, or dive straight into the series and figure it out as you go alone. I personally would recommend that you start with Teddygozilla; the episode's sense of mystery and intrigue makes you really wonder what the hell is going on at Kadic, and when it drops you into the middle of the action... well, it's quite a good feeling. Rather than having the rules of Lyoko given to you at the start, you have to figure it out on your own, and all of a sudden the reality that they live in becomes so much more flexible.
All things considered, I'm not too much of a fan of the prequel; looking at it as a new viewer, it poses questions instead of letting you figure out what the questions are yourself. That being said, if you feel a little lost with all of characters, or if you want to see their humble beginnings, by all means go for it. If I remember correctly, Part I of XANA Awakens is available for free on iTunes, and Part II can easily be found on YouTube. For that matter, the first two seasons in their entirety can be watched for free on Hulu.