This will be a tough one. My favorite is Mudkip, but also love Torchic.
In Emerald(my first 3rd gen) I chose Mudkip, Torchic in Ruby and Treeko in Sapphire (originally wanted Mudkip and Treeko reversed for the whole color matching deal, but since the first one I got was Emerald that got turned around :P )
They are all fully evolved and will be on my "main pokedex" in XY boxes. I don't like having multiple of the same evolution (problem in X if I ever get Leafgreen, have a Venusaur in X now and may have to keep my Bulbasaur a Ivysaur -_-; ), but I'm just sentimental to my Team Pokemon and too orderly. :P lol Probably 'Kip in Sapphire and 'Chic in Ruby, most likely, kept at 2nt stages and use their mega stones(IF Mudkip gets one) on my original fully evolved ones from original Hoenn. <3 :)