Thing is, if you drop these two amazingly developed, important characters, let's just say that the show will capsize. Yeah, that's right. It'll be ruined to the point of no return. Why so?
Applejack is not very popular. We all know that. She holds the title of being the only main six who had a joke made of her, having been called a background pony on numerous occasions. But. Does her popularity matter when seeing how the show will survive without her? Think about it. I don't care how popular she is in the brony fandom, she's vital to the show. In keeping her friends straight (i.e. not crazy), in supporting her friends, in being one of the Elements of Harmony, as many people mentioned before me. Applejack is the anchor of the group that holds them together. Without the anchor, the whole ship is pretty much doomed.
Rarity is not very popular, too. After being called many descriptive names after Sonic Rainboom, in which she tried to "steal" Rainbow Dash's glory, she was shunned to a side by many Rainbow Dash fans (and other fans, as well, but usually RD fans, from what I saw. Obviously, I don't mean most of them, but many of them did criticize Rarity quite a lot). She was also the only one of the main six who had no episode in Season 3. But, again--does popularity matter? I say no. A character who's essential to the plot, no matter what bronies think of them, should stay in the show. Rarity is a character essential to the plot. She inspires some of us to aim for the top. Yes, Rainbow Dash does that, as well. So why should we even look at Rarity? Because she does it in a different way that some bronies can relate to, while others relate to RD's way. I compared RD and Rarity cause the two groups are usually at each other's throats.
Anyway, children. The moral of the story is that you don't remove an anchor from a ship because the crew doesn't like the rust on the iron.