While I can understand the frustration, you can't really compare it to Pokémon showdown. In showdown, everyone that logs in comes for the same purpose, to PvP, so there is no problem for the system to not make you fight the same opponent in a row.
In pokemmo however, PvP is only one aspect. Players can be completing the story, shunting, gym rerunning, breeding, etc. So PvP matchups depends on how many players happen to be queuing at the same time as you. And if it so happens only a handful of people join the queue the matchups might end up being the same alot of times until more people join the PvP queue