I went through AO3 trying to find all of the one-shots primarily involving trainer/legendary Pokemon interactions I could and picked out the ones that I liked. Most are cute, a few are sad, and all of them tend to put the Legendary as the main focus of the story. Here's a sampling:
Lucifer (
http://archiveofourown.org/works/399718)- Giratina/Dawn
gods amongst humans (
http://archiveofourown.org/works/5396810)- Yveltal/OC
The Stag at the Pass (
http://archiveofourown.org/works/1180631)- Mewtwo/Xerneas/Serena
I'm Just A Dreamer (
https://archiveofourown.org/works/4892539)- Dawn/Darkrai
First Contact (
https://archiveofourown.org/works/2885906)- Deoxys/OC
Untouchable (
https://archiveofourown.org/works/3210068)- Deoxys/Brendan
Knowing and Understanding (
https://archiveofourown.org/works/2842964)- Groudon/May
Tiny Human (
http://archiveofourown.org/works/7898488)- Zapdos/Spark
SOSBT (
http://archiveofourown.org/works/3954397)- Suicune/Lyra
