I'm thinking about this same decision myself. 4G just got turned on in my area, and as a result, my Thunderbolt no longer comes anywhere close to lasting the day. I'm starting to feel like 4G isn't that valuable for me, anyways. For most tasks that I'm doing on my phone, it doesn't make that big of a difference, and I'm also near a WiFi access point most of the time.
I'm not all that in love with the Thunderbolt myself, though. If you really like yours, would an extended battery fix your battery issues? It honestly isn't as bad as it looks in the photos; one of my friends has one and it actually almost makes the phone feel better in the hand. I don't think I'm going to go that route for the reasons I mentioned above, but it might not be a bad avenue for you.
I think it really comes down to whether or not 4G is valuable (or will be valuable) to you. If you think you can go a year or more without 4G, going with the Droid 3 might pay off, as I imagine next year will bring less power-hungry LTE chipsets. Otherwise, the Bionic will almost certainly have a big battery to go with the rumored 4.5" screen, so it'd probably be your best bet.