I noticed from watching the RAW episodes that 4Kids often had a problem with keeping the ending BGM in the earlier episodes..
The sad piano music wasn't heard until episode SEVEN but it was heard I think almost 4 times before that. Also a piece that we don't really hear is the ending music in episode 3 - we heard that at the begining a lot, and I remember it when Ash won against Pete n round 2 in the Indigo League.
While they did keep a LOT of music in Indigo, they really did replace a lot too if you watch the raw.
Also I noticed Dogasu in your Squirtle comparison that it was stupid for Squrtile to just go with Ash...
The Squirtles were ditched by their trainers, and then when Ash sacrificed himself so that the Squirtle wouldn't get hit by the bomb he realised that he would be a great trainer, and decided that he was a caring trainer and wanted to go with him. I didn't think it was that bad of an ending/reason to go with Ash.