Regarding the edit, don't you need Rock Climb to get into Wispy Ruins in the first place?
Alright, so you rock climb into wispy ruins. You'll see water, so surf. You'll see a hiker guy on the left, head onto the land he's on. Then you'll need to rock climb some more. After I believe 2 rock climbs, head east, and you'll hit a waterfall. Keep pressing the "up" button while under the waterfall and you'll enter a secret room. Maybe you'll find a mudkip there.
Oh and you'll want the ladder later, trust me. (But that's not connected to finding the mudkip)