Leonard and Priya were never going to last long-term, as evidenced by her unwillingness to be open about their relationship. It always felt like she is using him for fun, not interested in anything too serious. Leonard is willing to be with her, but she doesn't return his feelings. Because of that, Leonard likely still thinks fondly of his time with Penny, and misses their relationship, which will lead to deeply hurt feelings at the Raj revelation. Moving forward, why would Priya want to stay with a guy who is preoccupied with his ex? They are likely over.
The Raj / Penny hookup is just a step too far. It is believable, but barely, and only because of the reasons mentioned above. Had circumstances been slightly different, it would not have happened. The event has no positive impact on the series, and is a huge downer to end on a season on. It should not have been done.
Raj moving in with Sheldon is a delightful side trip. It is too bad it looks like things will return to status quo by season premiere. Leonard is used to Sheldon, so Sheldon must go to extremes for there to be any interesting plot between the two of them. By contrast, while things at first appear rosy between Sheldon and Raj, there will surely be any number of obstacles the two will have to overcome to work out a truly peaceful living arrangement. As such, plot wise, it is much richer if Raj stays with Sheldon. Sadly, the chances of that are low.
Poor Howard doesn't need to be dumped on anymore. Granted, he has had a good year, as he grows closer to Bernadette, and they even get engaged. Not only that, Howard's surly mother (Carol Ann Susi) actually likes Bernadette a lot, and approves of their relationship. This may lead to the conclusion that Howard has finally achieved a perfect life. That would be faulty reasoning, as everyone has problems, and nothing is ever perfect.
Howard's main source of contention right now is how Bernadette overshadows him. He has always been arguably the weakest member of his group of friends. He is the only one, after all, who is not a doctor. Sheldon puts down Howard's research, and berates his chosen profession. With Bernadette, Howard thinks he has found a true partner on even footing, as Sheldon is equally skeptical of her work. But now Bernadette gets her PhD. Howard tries very hard to be supportive, but with his friends teasing him, it isn't easy.