A new version of iOS will not make it easier to jailbreak, that's foolish! Each time iOS is updated there are file system modifications and exploits get fixed. A new version of iOS complicates things for devs.
As a current owner of a jailbroken AppleTV2, my advice to you is to keep your ATV3 unplugged (so it doesn't auto-update, it happened to me!), and wait for an ATV3 jailbreak to release. These things take time, and there is no way to know when or how long a jailbreak will take to release.
Jailbreak developers are going to be working with the first iOS version on the ATV3, not all of the updates that are coming along afterwards. So in order to have your jailbreak soonest, NEVER update the thing until you know that if you update, you can jailbreak the firmware you're updating to.
My ATV2 is sitting on an untethered iOS 4.1 or something with updates disabled because I originally did not want it to auto-update, but now I just don't feel like fooling with updates and stuff as my jailbroken ATV2 does everything I need, and there are no new features that I need in the newer releases. Plus once you update, your jailbreak is wiped, and you have to re-jailbreak it, and re configure the device.
Just wait for a JB, and once you get it, don't fool with updates. There's hardly ever anything worth updating for.
I'm actually trading my ATV2 for a 160GB ATV1 this week because I don't want to deal with this jailbreak/update crap. The ATV1 is just as good as an ATV2 (does everything it can at 720p, AirPlay can be enabled, with hardware modification it can process 1080p video), and with upgradable hardware and mods, it's more useful to me than the newer ATV2, even at jailbroken state. I've read a lot on it, and I feel that the ATV1 is better for me.