One of the rules for the Greatest Ingame Monsters post was that I wouldn't include the starting Pokemon because it would've made the list nothing but a ranking of the various starters.
And while on vacation recently, it gave me a chance to sit down and do a full ranking of the starters. All of them.
Red/Blue, Fire Red/Leaf Green
A lot of this ranking came down to the general usefulness of the Water type over the best of the Grass type. In RBY, Squirtle is favored by all the speedrunners for its ability to learn the two good HMs and to abuse the crap of the $200 Ice Beam TM (look it up). And in Fire Red/Leaf Green, Bulbasaur might've picked up an early Sleep Powder but the old ingame advantage of being able to beat the first two gyms gets beat down thanks to a new Dark-type Bite beating down Starmie. Charmander, for all of its popularity and the FR/LG Metal Claw addition, just had a bad Gym arrangement for the Fire type (it beats 1 and pushes against another).
And ironically, it's still better for you than the Eevee you would've gotten otherwise.
Gold/Silver/Crystal, Heart Gold/Soul Silver
For all intents and purposes, the GSC starters are the worst of the bunch. Totodile has two major advantages over the other two: It has access to an early Ice move (Ice Punch in GSC, Ice Fang in HG/SS assuming natural movesets stay the same) and it hits final form at L30. Cyndaquil has no natutral variability out of Fire moves and Thunderpunch but it can't even pick that up until it hits final form at L36. And Chikorita... worst starter ever. Unquestionably. Sure, it's good for defense, but that's not what you look for in a starter. It can't even Sleep Powder, which if you can't attack is the least you ask for out of a Grass type.
The problem is that Totodile falls to Starmie/Lapras in GSC and the mandatory Red Gyarados in HG/SS.
The jump to the new stat system brought the toughest decision of the groups. All three are pretty strong, but the only time I ever bothered to do a solo-starter run, it was in Ruby with Torchic (eventually Blaziken). Since they all evolve at the same levels and work out well against the same number of Gyms, the deciding factor was actually how they would fare against the Elite 4 and champion - and Torchic wins that pretty handily.
Emerald really buggered things up for Torchic though - where it could hold its own against the Water gym, the new additions plus the Champion training Water as well knocks it to last. Mudkip's movepool gives it more variety than Treecko (and hey, STAB Earthquake in the final form - great success!) to give it the edge.
The biggest factor in Chimchar's success is the limited Sinnoh Pokedex in DP. Because of it, Chimchar can work well against practically every gym, and the original gym arrangement gives Chimchar the ability to function well against every Gym. Turtwig is a strong number 2 due to the natural Earthquake it gets as soon as it evolves into Torterra...
... and it's the natural Quake that gives him the win in Platinum. The Ghost gym going 3rd when he learns Bite in the early 20s works in his favour as well - the only gym he can't really be used in is Candice's, and even then he can still take out Piloswine with a type bonused attack.