The Marine Cup was just a tournament done for fun on a ship full of passengers. The Don George, Clubsplosion, and Junior Cups were obviously major events for serious trainers all around the region. It makes sense that the level of competition in the Marine cup was lesser and that Ash could easily pick up the win over a bunch of tourists. And honestly, at this point I'll take any official battles I can get. I would still like to see one more major tournament before the end of Best Wishes, but I'm doubting it will happen.
I think at the heart of the problem is the issue that Best Wishes can't decide if it wants to be about the battling (like Sinnoh) or the adventure aspect (like Kanto and Hoenn) of Pokemon, and can't fully commit to either. From a battling standpoint, for all the flashy animation the battles in Sinnoh were generally more intense, interesting and exciting, and the process of training and battling was thought out much more carefully. At the start of Best Wishes it seemed like they were going that route, but seemed to lose interest in Ash's training and his preparation for the league as well as his battles with his rivals around the fifth gym. From an adventuring standpoint, they've tried to include some interesting locations but Unova as a region seems to be more urbanized and you don't get that feeling you got in Kanto and Hoenn where the main group was traveling for weeks on end through mountains, forests, etc. between cities. With such a short distance between cities, there's not much room for danger and excitement.
I don't want to trash the Da Islands saga too much because I did like the second and third episodes, but it does seem like a sign that the writers are struggling to figure out where they want to go with this franchise. I guess the answer is just to save all their good ideas for X/Y, and I am hopeful they can learn from their mistakes in Best Wishes and the show will be better because of it.