My favorite starter from their respective regions are:
Kanto: Charmander (Charmander has an awesome, albeit slightly overrated, final evolution)
Johto: Cyndaquil (decent move pool and to top it all of, it has an awesome evolution family)
Hoenn: Mudkip (Mudkip is such an adorable pokemon, and it's move pool is pretty good once it evolves)
Sinnoh: Piplup (Even though Piplup can annoy me, its final evolution, Empoleon, is just far too awesome)
That pretty much covers my favorite starters from each region.