I like YIJC. That said, I have never believed Flannery as Indy. He's not terrible but I don't see Indiana Jones when I look at him. Also the "Henri Defense" name through half the series takes it even further from the character Ford plays in the movies. It had some great quality moments but again I found myself waiting for Indy from the movies to show up and he never does. The Crystal Skull while being the weakest movie still makes me feel like I am watching an Indy adventure and like I'm watching Indiana Jones. It has some cheesy moments but YIJC has tons of them too. So Crystal for me any day.
Oh, man. I enjoy all four movies, right up to and including Indiana Jones and the Kingdom of the Crystal Skull, weaknesses be damned - but I think The (Adventures of) Young Indiana Jones (Chronicles) TV show is absolutely brilliant. It's the most artistically ambitious thing George Lucas has ever done, and in my opinion his greatest creative work since at least the early '80s.
Better than Crystal Skull? Heck, I think Young Indy is better than Indiana Jones and the Temple of Doom, Indiana Jones and the Last CrusadeandIndiana Jones and the Kingdom of the Crystal Skull, and I love those. I think the show is better than any of the Indy movies that don't have "Raiders," "Lost" or "Ark" in their titles.
What do I prefer? I suppose KOTCS, because it's a proper Indy movie with Ford playing Indy. Then I remembered Mystery of the Blues, which features a few minutes of Ford as middle aged 'Snow Indy with Beard' which is pretty cool in a mini adventure, but the answer is still KOTCS because it's a full proper movie with Ford as Indy.