This is just a personal tracker, really, for the pros/cons of Cubone/Squirtle runs. Feel free to add on, however.
Lately I've found decent success in my Cubone/Squirtle tests, ignoring my horrid RNG that I suffered during my first run of it (which made me have to dump the run, I was on 4 hours and stuck in Mt. Blaze).
I know the general "good" runs like to be Meowth/Squirtle, and in the past was Skitty/Squirtle, though I've done some searching and found a lot of potential for Cubone.
Though Cubone doesn't get a damage move till level 9, Cubone will level up faster than the partner Pokemon in order to compensate, which I've discovered after years of playing PMD that player Pokemon will level slower than the partner. So it's already a nice change of pace for me when I'd like to be the group tank.
Bone Club is great for a lot of dungeons, though its low PP may get lots of players into a pickle. Luckily at level 13 Cubone learns Headbutt, which doesn't deal a great ton of damage, but at least its got PP.
Cubone can deal massive damage from what I've seen playing it, and a few Bone Clubs can wipe an enemy fast. Another pro of Cubone? DIG. Dig at level 17, which was around the time I got it, was dealing 50-60 damage on a normal hit, and 100+ on a supereffective. But, again, low PP.
I'm personally interested in Cubone's level 25 move, Bonemerang, because I hear that it's a killer.
With the good we already know Squirtle has, it's seeming to be shaping up that Cubone may be a great starter choice along with Meowth and Skitty, though I'll have to get some play in with them too.
On top of it all, starter Cubone can have Thunderrod. Which is a BLESSING in Thunderwave and Mt. Thunder! Fighting Zapdos is a breeze as Cubone.
Cubone sadly may be only good in the short-term, however, but I've got my hopes up, and I'm gonna try to push my test runs to level 25 (unless I get stuck in Mt. Blaze again).