You're definitely not alone. SonInLofOfSam and I just finished Hypertrophy 1 and, while I consistently enjoyed the upper body days, the lower body workouts became a chore with a week or so to go. I will confess that we only did the squat, deadlift, and crunch portion on the last few workouts and skipped split squats and step ups altogether. Having a partner is essential, but even then, I can only tolerate so much displeasure.
The long programs are definitely tough. Following the eternal beginner program, we did Break In 1/2 for 2 weeks each I believe, then Fat Loss 1/2 for 4 weeks each and they were fine. At 8 weeks, Hypertrophy 1 is a challenge. That being said though, I'm really looking forward to doing Hypertrophy 2 next -- not just because its a new program, but because there is more variation (3 workouts vs 2) and less lower body.