To be truthful I haven't been as into the show as I used to be but I'll still watch it when new episodes pop on. Alright alright let me try to describe the major parts that happened mainly in the beginning and ending of each season you missed. *I might copy and paste some of this from a wiki*
Okay so at the end of the second season, Twilight Sparkle grapples with her conflicted feelings when she finds out her brother, Shining Armor, is marrying Princess Celestia's niece, Princess Cadance. Twilight also begins to suspect that Cadance has changed since their childhood. A new villain appears through out the episode also. This all takes place in the crystal empire.
Alright onto the beginning of season 3, which is only 13 episodes. Kinda short I know. In this episode, a curse that caused an empire to vanish for a thousand years has finally ended. Princess Celestia orders Twilight Sparkle and her friends to help defend the newly awakened Empire against King Sombra, the evil unicorn who had cursed the empire. Then Twilight Sparkle and Spike search for the Crystal Heart while their friends try to protect the Crystal Faire from King Sombra.
Beep Boop onto the ending of season 3. Twilight Sparkle accidentally switches her friends' destinies and tries to fix them. By doing so, she becomes an Alicorn princess.
Here we go onto the beginning of season 4. Princess Celestia and Princess Luna mysteriously disappear right before the new Summer Sun Celebration. As Twilight Sparkle attempts to figure out what happened to them, the Everfree Forest invades Ponyville. Next Twilight Sparkle discovers the origin of the Elements of Harmony, and she and her friends seek out the cause of the Everfree Forest's invasion.
Ending of season 4 here we are. In this episode, Twilight Sparkle struggles with her sense of purpose as a princess when Celestia chooses Discord to help track down a new villain. In this episode, the other princesses transfer all of their Alicorn magic to Twilight Sparkle in hopes of saving Equestria from the diabolical Lord Tirek.
That is a very rough summery of what you missed. I left out the middle of each season because that would take forever to describe the minor parts. If you want more detailed details of the seasons I'll put a link to the wiki:
http://mlp.wikia.com/wiki/My_Little_Pony_Friendship_is_Magic_Wiki