Blue.
I prefer the box art for no other reason than A) I prefer blue as a color and B) Blastoise's official art is staring right at the player and gesturing towards them, as though saying "Come on!" Charizard, on the other hand, seems to be staring at a bug buzzing just out of range of the camera, totally oblivious to the viewer. It looks majestic, but Blastoise looks better.
Version exclusives:
Sandshrew is a solid Ground type, whereas I'm not sure Ekans is distinguished for anything but annoying people to death with Wrap. (Off-topic, but if you ever play the Pokemon: Team Rocket Edition hack, this is actually a strong reason to choose Ekans as your starter. Meowth's attack and Koffing's bulk just don't compare to the ability to completely lock down your enemies. Okay, back on topic...) Plus, Sandshrew is cute and bulky, whereas... Ekans is just lacking in good stats, as far as I can tell. It's okay, but rather ehhh, especially as BSTs increase as endgame approaches.
Victreebel has Razor Leaf, which is a guaranteed critical hit due to Gen 1's offbeat crit mechanics. That makes it essentially a 110 BP STAB move with 95% accuracy and no drawbacks. Vileplume doesn't. Vileplume is cuter and has slightly more physical bulk, but Victreebel is a better Pokemon overall. Plus, it doesn't have an absolutely hideous middle form.
Blue has the game's only natural free money dispenser. What's more, it's a natural free money dispenser that gets STAB Slash and has the speed tier to get 100% critical hits with it. Mankey, in contrast, doesn't even get natural STAB. (That would come in Yellow.) It's a decent Pokemon with TM support, but basically inferior to Machop/Hitmonlee in every way.
Honestly, I'd prefer Scyther over Pinsir just because it looks cooler, but I don't spend enough time in either the Game Corner or Safari Zone to see either. Likewise Electabuzz over Magmar -- but, again, I hardly see those. I'm pretty neutral on Arcanine versus Ninetales because the only Gen 1 Fire-type I use on a regular basis is Charizard, and then only if I feel like Charmander starter.
Basically, there's not much difference, but what difference there is tends to slant me towards Blue.