Yeah there are some differences but they are not consequent. The changes doesn't really affect the story as such.

For me, manga is always better. Forever. Why? Because manga is original, pure 100 % directly from Hiro Mashima. You can enjoy some scenes that you'll never found in anime. Example, the anime don't show bloods. Manga does. And that's more epic.
Hiro Mashima made soooo awesome drawing scenes. Example: (at the bottom at this post)
Which picture do you think is more epic? For me, the manga of course :)

Anime contains filler—though, until now Fairy Tail only has 8 filler episodes. And sometimes it's getting too much. Example, scene in anime when Natsu and Lisanna in the forest, Lisanna lost, and then in the end Lisanna ask Natsu to find her when she lost again. That's filler. Hiro Mashima never write that.

And, Hiro Mashima made sooo many awesome special chapters (80 % of it are Nalu ♥)

Why Fairy Tail anime got high rating? Because the anime following the plot of the manga. So, there never be an awesome Fairy Tail anime without the more-awesome Fairy Tail manga ^^

totally agree with RedFairyPanda manga is awesome

manga will always win no matter what you put it next 2 :)

*came here to talk about how good the manga is*
*reads Red_Fairy_Panda's post*
...
I don't think I need to add anymore, I agree with RedFairyPanda completely.

Okay. I think I'll be reading the manga from now on. Starting with Chapter 1!