I used AutoIt before AutoHotkey was created (when it had a syntax inherited from BAT files). I don't have enough experience with current AutoIt to make a correct comparison. It has a quite regular syntax, while AutoHotkey's syntax (although greatly improved from the original style) seems odd. People having never coded before actually love this syntax!
I hesitated, read numerous comparisons, and finally chose AutoHotkey despite its syntax. Partly because of its superior hotkey management, partly because it was open source. The author was active (he stopped, but there are alternative branches now) and open to suggestions. I shown a prototype of regular expression support using a PCRE DLL. He integrated the concepts and pushed them beyond (regular expression 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. The binary is compact and you can make a standalone EXE file with your scripts. It also has GUI support (good for quick simple dialog windows).
I won't say one is better, the choice is mostly a matter of taste, feeling and needs.
