I haven't seen How I Met Your Mother yet, so I skipped over your opinion of that one.
I too was disappointed with Bones. The first half of the season, I was hoping that Sweets was Gormagon/Gorgonzola

I really came to like the dynamic between Sweets, Bones and Boothe, so I was hoping he wasn't G or the apprentice. I was very disappointed that Zach was the apprentice. I felt like it was a last minute decision with no hints or clues in previous episodes to point us that way. I just feel like it was poor writing, but maybe I missed something along the way.
One Tree Hill is the only other finale I've seen. It was ok, but not great. The cliffhanger was stupid. They showed it on commercials, so I was surprised that was it. I assumed there would be more to it. I assume he called Lindsey because Peyton was waiting for a call from the singer about the man she met who know Peyton's biological mother and Brooke was waiting for a call to tell her that the baby was home ok. Of course, they could do something totally lame and have him marry Brooke so they can do something with that next season. I hope if he calls Lindsey she says "no" and is finally off the show. I don't care if Lucas is with anyone else, but I didn't care for Lindsey's character. Hopefully Dan is dead and not just hurt. His part in this season was aggravating and useless. Nathan's mom's character is just wrong! They've turned her into a total tramp and Skills into a male #####. I was very much not into that story line. It just seemed gross. Hopefully they'll get rid of her next season as well. They "kids" on the show are old enough they don't need their parents hanging around forever. It's like if 90210 had kept the parents through college and beyond. Totally pointless characters.