I really like this idea. I wish it was something you could do via a poll in the normal threads (like the previous "rate the song series") but I get that you want to do something more comprehensive. I'd actually prefer a "rate the live songs" series since that's never been done and it's the only way I listen to U2, but that would be a much bigger challenge, starting with which versions and sources to include.
I'd say include SOE. Why not? You want to rate all U2 songs, and those are U2 songs. Yeah, the results might be skewed a bit, but they'll be skewed no matter what. Yes, SOE might rate higher, but that might cause SOI to skew lower. Stuff goes in and out of favor in any case for all kinds of reasons (remember the Crystal Ballroom hysteria?), so I'd side with being complete over worrying about whether something is too new. Trust people to take what you're doing seriously and give thoughtful, not impulsive reactions. This isn't Twitter.
You also might want to consider reaching out to other U2 forums, including in other countries. I think the self-selecting sample you'll get here might be a little small to get the results you're looking for. Frankly if you don't have enough people participate, your demographic data (which seems like the whole point of doing it this way) won't mean very much.
Anyway good luck! I'm sure everyone will be interested to see your results.
Oh, and please disregard Axver's MOS rating.