I can see it both ways, a letter in every episode seems to be an important part and is a feature of the show. But also it can become redundant, I believe it should pop up randomly to keep the viewers wondering and guessing (even though it's a small 1-minute event).
You're looking at the guy who was first to notice this XD Anyhow, I suspect it's due to the fact that they're moving on from friendship lessons and into territory that touches other bases. It's not very good in the fact that it's no longer consistent with the name of the series, but moar ponehs es fin bye meh!!!11eleven!!!
"Dear Princess Celestia, Nopony likes you. Sincerely Twilight Sparkle" I'm guessing it went something like this....
I tend to agree with the consensus. Now that we are in the 3rd season and headed towards a 4th if a letter was written at the end of each episode it would cause the endings to begin to get stale. This might seem strange but one of the things i love about the letters being written back and forth is how Spike burps up the letters sent to Twilight. Most unique and funny way to get mail ever!
Maybe the team forgot to add them and felt bad, so they put it in two hopping we wouldn't notice, btw is it me or is Celestia getting less face time?
A few characters that haven't gotten quite so much face time in earlier seasons are getting more now, which isn't a terribly bad thing. Oh wait, I have a meme for this.
Even though Cestestia was in the Flutter On episode and it was unnecessary to write her in that one, Spike should have written a letter to her. I miss the letters to Celestia segments, plus I would love to see him write on then blow it to her.