disclaimer: I use AHK myself and have not tried KeyClone or others myself yet.

It revolves around how much time you got to make you setup. KeyClone is probably very fast to get going. AHK eventhough much harder to setup gives you a whole other level of flexibility. Since it can manipulate windows and place them and map keys/mouse as you wish you can do pretty much everything you can dream of in AHK.

Examples what i mean with flexibility:

1. You could have the numpad (on the keyboard) emulate a cellular-phones T9 input method when your mouse pointer is in the lower right corner of the screen but work as normal when the mouse pointer is anywhere else.

2. You could have you keypresses routed to the "action bar" ingame that is nearest your mouse pointer.

Not sure if this would ever be useful but it's examples of what you can do when you write it yourself.
I'm pretty sure the above mentioned functionality would be pretty hard to achieve in most other ready multiboxer packages (unless the author specifically add such a function that can be enabled in the config).

There is yet another aspect to: AHK allows for a very high degree of automation (being a general purpose script language and all) so you have to try to think about functions you do to follow the spirit of the WoW ToS all the way. Blizzards rule is (simplified): Never automate something into less steps (keypresses/mouseclicks etc) than would be possible to achieve with the original GUI (or through the Addon API).

I'm however pretty sure that AHK can do most of what the ready multiboxing packages can do, if you got the time to code it yourself. I don't think the language itself will be the limitation for implementing any of the features you need.