If I start with a mudkip as my leader can you tell me which is a better..

Torchic is because it will have two type fire and fighting

I would say Torchic but the best partners are Grass-types and Pikachu.

Well, I think Pikachu is a perfect partner, because they're who I used as my starter and partner! Seriously, it depends on whether you'd rather have fighting or flying as your eventual dual-type, really. Mudkip will be Water/Ground eventually, so he can walk across water, and either fire-type will be able to walk across magma, so that's good, but the flying part may also come in handy (I'm not sure if Charmander will eventually be able to float or not, since he's a combo and I don't have him in my game, sorry, but I don't think so! But he does get Metal Claw at
Level 13 and Flamethrower at Level 31!) but fighting is good against normal types. Remember, you won't be able to evolve them until you beat the story mode, so you're stuck with the moves they get as their first evolutions-another consideration, unless you use TM's. It's a choice of what you like better, when it comes down to it. Good luck deciding!