They're similar in terms of flexibility, but they differ both in terms of design principles and of implementations. The FATE family is often introduced by the phrase 'it models fiction, not physics', which is to say, it models genre fiction. Contrast against GURPS, which would firmly be described as 'models physics' *mostly* genre-agnostically, with genre conventions usually plugged into that on a per-need basis (or not at all, producing a 'literary fiction'-like or 'nonfiction-like' effect).
There's also the Lego vs. Plasticine factors. Whereas in GURPS, you'll often find additional toolk…