They are both valuable for lower body fitness. Squats are more about strength-building, lunges are more "functional."
This article is good.
I think lower body conditioning for strength, endurance, and athleticism ought to include (not all on the same day) barbell squats, leg press, kettlebell lunges, stair machine (which is good cardio also), deadlifts, box jumps. I do sets of each just once weekly. No time for more.
I omit mentioning cardio exercises which use legs (all of them do) because the emphasis of cardio is, obviously, cardiac fitness.
Lunges with weights are easy to hate. Gotta get in shape, though.