Nothing turns me off to a game more than the concept of NPCs that are always more powerful than PCs can possibly become. I detest these types of characters in Forgotten Realms and I can't even begin to consider playing anything put out by White Wolf for much the same reason.
So, no, I don't see Vin as "over the top and unbalanced" or as a "poor PC". The poor PCs would be the ones that basically spend their time on the sidelines cheering on the heroes of the story.
... thanking the gods he never had to wear pom-poms to cheer on Elminster and Blackstaff in a game ...
Okay, I've been mis-understood. Not every padawan is Yoda. Not everyone who picks up a sword is going to be Conan. Not every wizard who ignores their studies to learn by doing is going to become Gandalf. Not every merchant is Han Solo, nor every bounty hunter a Fett. By the same token, not every Mistborn should become Vin.
Should you be on the side-lines? Not even as the healer. (Especially not as the healer, you're needed in the thick of battle, where the wounded and dying fall.) There should NEVER be GM-fiat NPCs.
But, when you become the most powerful beings on the planet, it's time to either move on to being the smallest fish in a bigger pond, or to retire. For all its flaws, imagine a Vampire game where the only vampires were the PCs, and everyone else was a normal human, and skeptic of the existence of vampires. Yawn-tastic. If ONLY Mistborn have useful abilities in the game, then players will only be happy with Mistborn. For the reason you pointed out earlier - most of us aren't happy on the sidelines. Characters like Grey Mouser or Subotai are fun every once in a while, but if I feel like a DnD 3.0 bard then something's wrong.
Disclaimer: I actually TRIED a bard; unless your GM is a combat happy type that suppresses role playing and social elements, it isn't as bad as all the blowback the class has gotten. Second ONLY to the rogue for urban adventures.
I could point to any number of games with 'rare' or 'exotic' classes/races that were common among the PCs because they had become the only classes/races worth playing.
But I'm off track (as usual). My point is that Vin isn't popular because of her powers (not with me, anyway). Vin and Kelsier are interesting because they remain human IN SPITE OF their powers. Because they are flawed, and can be hurt. Not 'I'm covered in sexy blood (Die Hard)' hurt, but actual 'We don't try that because we'd DIE' hurt. Each character you could point to in the series has their flaws, their failures.
Mechanically, I'd like to see Allomancy broken up into class features, Feats, and WP (weapon proficiencies). Maybe gear picks, also. Which tricks have I brushed up on enough to use readily?
But take a look at Spycraft - the Wheelman and Hacker and Advocate shine at different points, but each one has their point to shine. In their element, each one is AWESOME. But none is so single-mindedly into their element that they're useless outside it. (The way old DnD magic-users were in an Anti-Magic field, for example.) This is the sort of balance I'd like to see in Mistborn RPG.
Behold Cett: Legless. Crippled. No Allomancy. Ruler of one fourth of the known world, and feared. One of four contenders for ruler of the world. I respect him more than many other characters more iconic to the Mistborn trilogy. I should be able to play my non-Allomantic PC in a party containing an Allomancer and a Feruchemist, and have the same respect for myself, even if my area of excellence is different than theirs.