One possibility is that the story could explore how Gwen's personality changes when she has the Omnitrix. She might become more confident or more responsible. Also, there could be new villains who are attracted to the Omnitrix now that Gwen has it. She would then have to face these threats and protect the Omnitrix from falling into the wrong hands.
In this fanfiction, Gwen might use the Omnitrix to fight new and unexpected villains. She could transform into various alien forms and discover new powers within each transformation.
The story could start with Gwen unexpectedly getting the Omnitrix. Then, she might start exploring the different alien forms she can transform into. She'd likely test out their powers in various situations, gradually getting a handle on how to use them effectively.
One possible antagonist could be an alien bounty hunter who wants to take the Omnitrix from Gwen for his own purposes.
Well, he'd probably be super OP. He could transform into all kinds of alien forms and use their powers in his battles. Imagine Naruto using Heatblast's powers to fight against Akatsuki members. It would be a whole new level of combat in the Naruto universe.
Well, it could be that his friends have to step up and protect the city while he's sick. Gwen and Kevin might have to deal with villains on their own, and they could struggle without Ben's usual power. Also, Ben might be really frustrated because he can't use his powers as he normally does when he's ill.
One reason could be that in the fanfiction, Ben is getting a lot of attention from other characters. Maybe the story has Ben in a romantic relationship with someone else, and Gwen, who has a close bond with Ben in the original series, feels left out. It could also be that the fanfiction portrays Ben in a heroic light without much focus on Gwen's role, making her jealous of the spotlight he's getting.
In this fanfic, Ben and Gwen might have various adventures at the resort. They could discover a hidden part of the resort with some strange creatures. Ben might use his alien forms to deal with any problems that arise, like if there's a malfunctioning pool cleaner that turns into a mini - monster. Gwen could use her magic to help keep things in check and maybe they make new friends among the other guests or staff at the resort.
It's not common at all. Most fanfiction tends to follow the more positive and popular pairings or storylines within the fandom. The idea of Ben getting Gwen pregnant is rather controversial due to their family relation in the source material. Writers usually prefer to write about things that are more in line with the general mood and values of the fan community, which doesn't really include this kind of rather odd and potentially uncomfortable scenario.
One possible storyline could be that they face a lot of family drama. Their families might be shocked and have different reactions, some may be supportive while others are against it. It could also explore how Ben and Gwen deal with the sudden responsibility and how it changes their relationship from just being cousins to co - parents.
An old enemy of the Omnitrix's creator could be a great main antagonist. Maybe this enemy was locked away for centuries and now has escaped and blames the Omnitrix for his imprisonment. He would be extremely powerful and have knowledge of the Omnitrix's weaknesses that Ben doesn't even know yet.