It's about preference I guess: Kohana takes advantage of a lot of the PHP5 extra's and also unfucks some of the "gotcha's" CI had (especially in the area of loading stuff). Also it is updated more regularly and is community developed.
CI is still good, I personally prefer Kohana's way of doing it.
EDIT: Just realised that I'm asking you to sum up a lot to recommend one over the other. I'm currently looking at both in detail, cheers.
In terms of LTS: V2 is pretty frozen at 2.4 right now (i.e. no API changes) though the documentation still reflects V2.3. There should only be bug fixes on the 2.x branch. 3.x is in active development (and worth looking at) and should be there for the long haul.
I personally use 2.x because that is what I started with and I haven't had chance to make the switch to 3.x (it's pretty much the same except there are changes to some naming conventions and file paths) mostly due to having to support 2.x based sites still :)
EDIT: It's a bit old (and I apologise for the abysmal writing!) but this is a comparison I wrote when I first made the switch: http://www.errant.me.uk/blog/2008/06/framework-comparision-c... might be useful.
Good luck and godspeed on the migration, AMO.