This is an interesting idea, and I'm curious to see where you go with this (also excited to see Heracross come in!).

At first I was really confused as to who Ami and Tintri were (and which was which). I think that should have had a bit of explanation rather than just saying the names (if this is related to another story, I haven't read it, so a brief bit explaining it would be good).

I liked the description of the town. I think some parts could use more description, such as when the totodile was stolen. You could also put more description into the actions of the pokemon, which will also give them more personality.

Interesting that the crystal onix was mentioned. I wonder what role that will play in the story. I was also surprised that mega evolution was a part of this. I think you should have the story explain how and why they have that.

Your spelling and grammar was good and I didn't see any typos or any really weirdly worded parts. And you seem to write a lot of stories here. Keep it up!