I think ArcisCannae summarized well the differences.
I used AutoIt because AutoHotkey (AHK) was created, when it has a clumsy syntax inherited from BAT files... I fear I don't have much experience with current AutoIt to make correct comparison. I know it has a quite regular syntax, while AHK's syntax, although greatly improved from the original batch style, is quite clunky and seems odd to programmers.
Funnily, people having never coded before actually love this syntax!
Personally, I hesitated a lot, read numerous comparison articles, and finally chose AHK despite its syntax, partly because of its superior hotkey management, partly because it was open source. Author was active at the time (looks like he reduced a bit the rate of releases but still work on it) and is open to suggestions: at a time I shown a prototype of regular expression support using PCRE DLL, and author integrated the idea and concepts and pushed them beyond (RE support in window name detection for example).
Documentation is excellent, detailed and full of examples with a comprehensive index; the community is very active and helpful; binary is compact and you can make a standalone exe with your scripts.
It also has a nice little GUI support, good for quick simple dialogs.
I won't say one is "better" than the other, the choice is mostly a matter of taste, feeling, needs...