Er, if this is still open...
Persian. Hands down. Has been my favorite since RBY (I even had my friend who owned Blue trade me a Meowth when all I had was Yellow), probably will continue to be my favorite. Forever! *huggles Rei-chan, my Persian in Fire Red* I also like Meowth by association, but not as much as Persian.
Other favorites...well, I think like Katie-san, mine shift, generally based on what I'm writing about, what my RP characters have, or who's on my current game team. Currently, I really like the Weedle line, the Chikorita line (probably my favorite starter line), Ekans/Arbok, Seviper (I'm going through a snake phase @_@), Skitty/Delcatty, Tropius, Nincada/Ninjask/Shedinja, Spinerak/Ariados, Ledyba/Ledian (I think I'm also going through a bug phase), Castform...maybe more...-_-;;
For some reason, I generally like bug and poison types more...also grass times and normal types. I somehow steer away from fire and dragon...@_@ (though I have a Charizard in Fire Red, but that's partly because I wanted to match the cartridge color) I also generally don't use Eevee lines in RP (though I have a Vaporeon on my Fire Red team) and legendaries anywhere. Yeah...
Oh! But out of the Shino Pokemon (I'm putting them in a separate category since we don't know much about them), my favorite is Buizeru (squeeee! *glomp*), and has been since it was introduced. I also really like Pachirisu, and a bit less than that, I like Cherimu and Pochama.
So if they're really all early-game Pokemon, I think my early-game team is going to consist of Pochama-chan, Buizeru-chan, Pachi-chan, and Cheri-chan. @_@