So I ended up playing with all three eventually, and this is how it went.
First time playing Sapphire:
"ERMAHGERD It's a Phoenix! This is going to be so cool! And ew what is with the green thing?"
SO I went with Torchic, and ignored Mudkip I believe. I was seriously hyped to see what kind of flaming bird I'll get.
Around 16th level: "Ugh, um, okay, a fire chicken...that's alright, fire phoenix is up next!
30+ level :"What the? Where is my Phoenix?! What did I spend 20 hours training this for!! What is this?!
I really wasn't expecting Blaziken to look like that but oh well.
On my next walkthrough Idk, which one exactly I took but I believe it was Mudkip, it was sort of cute and goofy so why not. Murshtomp was a bit odd, but Swampert was a beast.
The last one was obviously Treecko, I wasn't TOO happy to have it but man, Sceptile was a pleasant surprise!
My favorite would probably be Mudkip, seeing one always brings memories back so year. K, well, all three of them do, but Mudkip is my favorite :D