I agree, Half-Life was recognized as a great fps, but not as earth-shattering or genre-breaking. There were LOTS of good, story-driven, technologically advanced FPS games before HL, and JK is a good example. Dark Forces was great too, as was Strife, and quite a few others.
In fact, JK is a better game than HL in every respect except multiplayer. And they got its awesome sequel out years ago!