Agreed. Outside of grovyle, I didn't enjoy EOS's story much... Team skull was what killed the story for me.I still feel like the only person who didn't think Explorers had a good plot. At the time it was the best story that pokemon has ever done (up until Gates to Infinity), but that's like arguing about being the tallest man in Lilliput. I'll discuss via the characters, as the quality of the characters generally dictate the quality of the story.
The Partner: Boring with a capital B. He really only had two defining features to him - he wants to be an explorer, but given that the series is about going on adventures, that is kind of a given to begin with. The second one: he's a bit of a wimp for the first quarter of the game, and thus uses you as a crutch and this was just annoying. My presence in the game felt entirely incidental during the first third, just getting dragged around by the partner's wishes, and most of what happens during this part was merely isolated incidents that contributed very little if anything at all to the overall story. If I have to ask the question 'why would I want to befriend you?', then there's a problem.
The Guild: Pointless, essentially just a bunch of walking verbal tics, and it's outright shameful how much time they take up considering how little they're actually involved in the plot. They rarely seem as though they do anything meaningful with you, and none of them go into a dungeon with you save for Bidoof and Chatot in one-off story moments. The only one who got any actual development was Chatot, and even then it was minor and didn't really contribute anything.
Dusknoir: Obvious villain, I mean, just look at him! However, I might have have been thinking that it was setting us up for a 'don't judge by appearances' moral if it weren't for that 'did Dusknoir just hide a smile?' point where you tell him your name. Then he became Mr Obvious Bad Guy for sure. Then it really became his only defining feature and really just served as an obstacle for you right until his last moments where he reveals that it's the fear of death that was driving him. Just mentioned though, never discussed.
Grovyle: A fan favorite...another fairly dull character for me. Probably the best character in the game, but not by much, but what kills Grovyle for me is his stoicism. I'll admit here, I generally dislike stoic characters on the whole, but for a big reason - if they aren't seen getting passionate and emotionally involved in what they're doing, then how can I get emotionally involved in what they're doing? I mean, there wasn't even a happy expression for when he is reunited with you once you make it back home from the future, let alone a teary-eyed one. That being said, he was still rather flat and has a lot of 'because the plot says so' moments, such as not saying 'Hey! I'm trying to save the world not destroy it!' while he was collecting the time gears, and a golden opportunity for intense build up was missed when he revealed he came to the past with a friend right before it was revealed that it was the player. If he mentioned it when they escaped from Dusknoir when they first arrive in the future, the build up would have been intense!