As one of the few female voices here I'm going to disagree on the Madonna episode. I was no big fan of hers when I was a teenager, but I think she has stood the test of time. She knows how to remake and reinvent herself in a way that few artists from that era have managed. Madonna isn't still around today because of her great musical talent, but because of what she had to say and how she said it, and how she chose to market herself.
If you do listen to her songs, especially the earlier ones, a lot of them are about young women finding power and discovering their identity in their sexuality, which, IMO, makes it a perfect topic for Glee. (Express Yourself being the best example of this.)
Also I'm surprised there isn't more love for the utterly amazing performance by Jane Lynch in Vogue. She is 50 years old, and she out Madonna-ed Madonna. She sang, she danced, and she looked fantastic while she did it. She is a brilliant, fearless performer and my admiration for her goes up every week.
I also thought Like a Prayer was terrific and I'm delighted they included a choir -- it's always been what made that song work.
The first two episodes were a little frenetic plotwise, and yes, there was some resetting, but showrunners can't seem to win on this one -- if they provide a satisfying conclusion at the end of ep. 13, but get picked up, they get grief for the "resetting" of stories to allow the show to continue. But if they leave lots of threads hanging and get canceled, they get pilloried for leaving viewers hanging. It's pretty hard to have this both ways -- TV budgets don't generally allow for shooting multiple endings.