I have decided to take your suggestion, I will replace Mudkip with Kabuto and Tympole with Omanyte.
As for the other spawns mentioned at the bottom, I can only fit so many good spawns on one map.
It's possible for one spawn set to have multiple sets in the future, example is rain having 2 of them, Trick room as well, etc.
There are many spawn sets yet to be seen, and will likely encounter the same problem of "why isn't this here?"
Anyways, thank you for the suggestion and have a nice day.