I admit right away that I never liked this pairing (and no, I'm not a Sheldon/Penny shipper). Leonard's interest in Penny always seemed purely physical and Penny's sudden attraction to Leonard came out of nowhere for me.
But the last two episodes where the final nail in the coffin for me. In episode 19 "The Wheaton Recurrence" Leonard tells Penny that he loves her, but she only manages a rather weak "Thank You" and then feigns sleepiness to avoid further talking. Later she claims that she doesn't want to say it too early since she did it once and it ruined a previous relationship. I'm sorry, but how is dating and having sex for 9 months too early for saying "I love you"? At the end of the episode, after much passive-agressive whining from Leonard and Will Wheaton claiming, that he wished the girl who didn't say I love you back to him hadn't strung him along for two years, Penny tearfully breaks up with Leonard in front of his friends and runs of without ever talking with him.
Then last Monday we got the aftermath of the break up in episode 20, "The Spaghetti Catalyst". Leonard is mopey and heart-broken, while Penny seems rather unaffected by the whole thing. It seems like she's more upset that she made Leonard feel bad, rather than beeing upset that their relationship is over. Heck, when Sheldon tells her that Leonard has been crying she seems surprised. Really, now? How stupid did they make Penny that she is surprised that her ex-boyfriend is crying after getting dumped in such a manner, after he told her he loved her no less. Heck, does Leonard even know why he got dumped? Because I don't see any evidence for that. And what is her reason anyway? Does she honestly not love him and knows it, so she thinks this is better than giving him hope where there is none? Considering how non-affected she seems about the break-up, it actually seems that way. She's more worried about things being awkward, rather than missing Leonard or being sad about the loss of a relationship/friendship.
I also don't buy Leonard being willing to be friends again with Penny that fast at the end of the episode. Some people have claimed that the time between the episodes is the equal to the time that passed on the show, but I don't buy that neither Sheldon nor Leonard have run into Penny for the last 3 weeks, considering she lives right across the hall from them. And while he first gained some brownie points with me for listing kind and funny as two of Penny's qualities, he immediately lost them again for suggesting that he and Penny be friends with benefits and when he gets a no to that, trying to cover it up by claiming that he was just joking. Just shows where his priorities lie.
Honestly, that whole break-up is bullshit from beginning to end. It's like the producers know just how boring their relationship is and that is wasn't going anywhere and they never seemed to know what to do with them as a couple. Their solution? Make them go back to being friends, but leave open the possibility for another Will They?/Won't They? (and Do I Care?) circle, by making them break-up over basically nothing so they have no reason to not get back together, if the writers decide to give it another try in the future.