Mootools 1.2.4 is not a Joomla 1.6 issue! I don't know where you got that idea from.
Mootools 1.2.4 is the latest is a long line of improvements to the Javascript tools used within Joomla 1.
5 There is no inclusion of Mootools 1.1 in Joomla. Mootools 1.1 disappeared from Joomla several version ago (I don't know which one it was but I looked at
forum.joomla.org
and there were many arguments 2-3 years ago about the problems this seemed to causing the community) therefore, if you are using Mootools 1.1 then you have some extension that has installed this.
What we are trying to say is that there are many people who are using old, clunky, outdated, unsupported odd-ball extensions that, one day, are going to cause them problems. From what I've seen, there are around one-in-five users who are still running legacy mode on their Joomla 1.5 websites! This is nearly one-and-a-half years after Joomla.org pulled the support plug on J! 1.0. So, the fact remains (and I accept the rationale) that, for some people it's not going to be easy to upgrade to K 1.6 and K 1.5 will have to stay as a fall-back option.
By the way, K 1.5.9 is extremely dated! If you want to stay up-to-date, you should be using K 1.5.13 at the very least.