I find that the AutoIT syntax is more structured than its AutoHotkey counterpart and this is something that can be useful to create and modify bigger automation applications. But, the difference lies in the fact that, for a casual-user, AutoHotkey is probably easier to get started with and to work with. It is also more powerful than AutoIT when it comes to managing hotkeys linked to simple actions (keyboard shortcuts).
So, if you intend to create full-featured automation applications, I would suggest AutoIT. But, if your intention is to create simple keyboard shortcuts, I would suggest AutoHotkey. Some examples of the latter would be using a hotkey to open a folder/document, start an application, insert text, show a webpage, use an extra clipboard, run an Excel macro, etc.
Update on February 7, 2018: For many users, who may only need simple keyboard shortcuts, installing and learning AutoHotkey, and keeping up to date, can be overkill. ShortKeeper—a lightweight software utility—lets you manage an AutoHotkey based system in a way most non-programmers will find remarkably efficient and effective. And it’s free!
By Denis Lamarre