Chikorita and its evolution's are support Pokemon.
Give it say Toxic, Giga Drain, (it's Attack and Sp. Attack aren't that far apart), Reflect/Light Screen, and maybe use it for a HM.
Totodile is a physical beast. You'll want to give it Waterfall, Ice Fang, and two other physical attacks of your choice. (EQ would be ideal.)
Cyndaquil and evolutions are all Special Attacks. Eruption/Flamethrower is going to be your main power source. All of its other attacks are pretty much physical.
Going with Cyndaquil would make your journey through Johto easy, and Chikorita a little more difficult. I know I made it sound like 'Quil's movepool isn't all that great, but it would be the best choice. Totodile is just there, in the middle for an intermediate level of difficulty.