From what I've read of your post, it seems that you have quite a few beloved characters to work with, yet no story to act as a vehicle for them.
In that case, I'd suggest that you study up on stories and their structures, especially in literature. As good as comics and tv shows are, they don't lend themselves as well to concise and compact story-telling--something that literature does really well, especially with shorter works.
More importantly, have a look at the stories that really impacted you, and see if you can learn from those ones.
I remembered reading Franz Kaka's 'The Metamorphosis' for the first time. It fucked me up so hard that I was left obsessively thinking about it 2 weeks after reading it--I had never witnessed in my life a story that ended so miserably and hopelessly.
The act of reading it and its contents weren't pleasurable at all--yet it stuck in my mind so much that I even named my protagonist after the author.
The reason it was so memorable was because it was emotionally charged and had something to say--in this sense, if you want to end up making stories that you like, ensure that it's something meaningful, both to you and your audience.