first of all you have to beat all gym leaders. tohjo falls does not lead you to the Pokemon league.
in the middle of the pond
There always is. it is a small dried up hole in the very middle of the forest area.
in the middle because tthere is more water.
in the pond
Not a pond as much as a lake. Lake of Rage.
in caves that have a pond in them
Whiscash Pond is not in Pokemon Mystery Dungeon: Explorers of Time/Darkness. It is in Explorers: Red/Blue Rescue Team though.
It is a pond with many high level magikarp and one level onehundred magikarp.
first you must have beaten Cyrus and met dialga at the spear pillar then you go to lake valor near pastoria city then you surf to the middle of the lake there will be a small island go there and into the entrance walk in to the middle of the oddly shaped pond and he will be there
look for a pond or lake with an island in the middle of it and hunt from there.
the Pokemon was azelf or it could have been mespert or uxie one of those
im not so sure that you can recruit squirtle in waterfall pond. in the beggining of the game he is a starter pokemon or he can be your partner