I imagine it's a number of factors. The big one I feel is the same as Bleach, where early on it's a bunch of small little arcs/stories that don't interconnect too much, which allows you to build a foundation and make the rules. However, as time goes on and you expand more upon the world, there needs to be at least an outline of a plan to go along, and at the same time not change the rules. With Fairy Tail, after a certain point it felt like Mashima wanted arcs to be bigger, but didn't care about keeping rules and other stuff consistent. So when we get to later arcs things happen that make no sense from what we already know of the world. Another major problem comes with the general theme and style Mashima went for after a certain point. His central point of friendship isn't necessarily a bad point to make, but when that's your only reason the guild comes on top every single time makes for terrible writing, especially when giving a power boost to beat an enemy you could do nothing against beforehand. Using One Piece for a few good examples, the idea of friendship was used in a few better ways. When Luffy fought Lucci and was down for the count, Usopp motivated Luffy to get up one more time. Lucci was also pretty beaten up, and it was down to the wire, so a last minute push for a final hit works, especially with the central idea of saving Robin and everything surrounding that. Another great example which didn't involve having someone actually win was in Zou, when you found out that the Minks withstood all the torture and refused to give away the location of their friend. Now that's a true message of friendship, where you do everything you can to protect someone.
Then lastly, Mashima wanted way too much fan service in this series. There were so many moments that were supposed to be tense, but Mashima just could not hold back focusing on butts or boobs in various shots. One that I will always remember was in the Grand Magical games, where Lucy and other summoning girl were about to fall in the lava, but the knight saved them. Should've been a cool moment, but there was an emphasis on their butts and the fact that the guy was pushing them up by the butt. Another big one was Brandish and Lucy being in the bathtub together. This war to determine the fate of the country is going on, but we need to show these two people naked in the tub together.