Abarenbo honey
Both couples in this story are adorable in their own ways. The first couple, Kuma and Hachi are a more stereotypical omega x alpha couple. Their initial encounter is a little questionable, but they eventually become a sweet and devoted couple, supported by Hachi's family. The second couple, Mitsurou and Suzume are less typical. Suzume, the alpha, might be younger, but he understands how important Mitsurou's independence and control over his body is to him and doesn't take advantage. He waits for years and continues to ask consent. Seriously, if only more omegaverse stories could be like that! And it isn't any less wonderful for the consent. If you are looking for a sweet omegaverse story, there are few on par or better than this.
Sayonara Alpha
I don't generally do shotacon (cause it's weird as heck to me), but this is a really sweet omegaverse story. The omega is a high schooler and hiding it (because omegas in the omegaverse are rarely treated well) when he meets his destined partner. Unfortunately his destined alpha partner is an elementary school kid. This kid doesn't really understand any of it, but once he realizes what they are to each other he is definitely one of the best alphas ever. A little angst but good and no real shotacon (at least so far).
Tadaima, Okaeri