Spoilers (as though it matters): I agree with every decision they made in the storyline, and I thought it ended the only way it could have. L dieing was a surprise that caught the readers by surprise and got people to either completely love or totally hate Light... and though I personally was on Light's side through the whole thing, I feel as though they had to have him lose at the end. They did something similar in Final Fantasy 6, one of my top 5 games of all time, where you fail to save the day half way through the game when you think you're about to confront the final villain, he destroys the world, your team is scattered and you have to regroup in order to finally take him out. It wouldn't have been the epic experience it was if you hadn't lost the first time around, and the victory wouldn't have been so sweet if it wasn't as built up.
People get upset that Light lost but having him win twice would have been redundant. I appreciate that they decided to have him lose due to his overconfidence and reliance on others to do his dirty work rather than simply being outsmarted. In fact, he was the one who outsmarted his opponent, it was only due to the special circumstances generated by the sacrifice of one of his rivals that severed his communication and lead to his ousting. Some people don't appreciate that he freaked out and begged for help at the end but I say he had that coming too. You spend so much time being totally overconfident and perfect only to end up losing everything you have in one brilliant instant and you freak out. It was also a great moment for people who hated Light, as you got to see him totally helpless and hopeless, so it provided some much needed fan service.
One of the best stories I've read and watched the date (I read it, then watched it, then bought merchandise for it).