I could not think of a tl;dr for this: please bear with me. This continuity is near and dear to my heart, and as such I am delighted with the idea of agents from it. As such, I couldn't help but give this as much thought as I could.
'Wow' I: yay, Sanderson fan! I'll admit to not having read everything by him--haven't read the short works or Alloy of Law yet, and I refuse to touch Wheel of Time with a Standard Adventurer's Ten Foot Pole, but he is one of my three favorite authors, at least in genre.
'Wow' II: I'll attempt not to use spoilers here, but we shall see.
1: Mistborn) Mistborn have special cloaks that tell people walking past them, especially at night, "Hey ho a Mistborn passes here." It's as much a warning as any Scalloped Bat-Cape throwing a shadow in the dead of night, giving the heads "and some Bat-operative, the Man himself or not, will stop All Crime Found Here." Noble houses covet Mistborn. Hell's bells, they covet any kind of Allomancer. Allomancers can seem very common in the books, but remember that we are following a group specifically gathered to be a combat strike team of Allomancers, and against groups which similarly gather them. Consider the non-nobles/government/Kelsier-gathered population: the numbers of Allomancers are much lower, let alone Mistborn.
Mistborn are a commodity. They are precious. Unless in a situation with many of noble houses are in attendance--and we know how few people are actually in noble houses--very few people will actually see more than one Mistborn at a time in their whole lives. Kelsier and Vin are The Notable Exceptions To The Rule, as they should be by being PCs.
Besides, as far as being Mistborn goes, if I am not mistaken by Alloy of Law being Mistborn proper is not something that really happens anymore. Twinborn seems to be slightly more common than Mistborn had been in Vin's time, though still quite a bit rarer than single-metal Allomancers or Feruchemists.
Addendum: um, having only the metal brought from HQ is... not a limitation. Any Allomancer or Mistborn only has as much metal as he's brought with him on any given excursion, or else that he scrounges up between resupplying, and the latter can be dangerous. That isn't a Special Limitation, that's just life as usual. Besides, a lot of Agents carry bags, or even Bags of Holding. You could dump a LOT of Allomancy metal in there. Not the best sell on that one.
2: Radiant) There used to be many. They are, however, figures of legend, and being a Shardbearer is incredibly rare. Remember what some of the lengths gone to obtain them are, and how high the value stakes of what people have given up or demanded in exchange for a Shardeblade or Shardplate armor is. I'm specifically remembering the truly poignant incident towards the end, regarding the fate of a platoon. Radiants are currently legends, and one reason several characters in that book are so visibly pivotal is because of the implication that they are Radiants, which haven't been seen in... a very long time, possibly centuries, that I do not recall off the top of my head.
Beyond that, we don't actually know yet how Stormlight works, thanks to Sanderson's brilliant ability to have us learn along with the characters how their magic works. I'd hesitate to make a ruling on use of it in any direction until that is elucidated; at best I'd say "He gets a supply brought with him from home but it will run out if used." After all, we have no reason to believe at this point that Stormlight is found outside that universe, or even on that particular planet (as we have seen no indication of it in the other three worlds of that continuity).
Even if there were thousands of Radiants once, consider how many people are in the Stormlight world. There feel to be far, far more, population-speaking, than in Elantris or Mistborn (though Warbreaker feels to have rather a lot too). Even if by numbers this were more comparable to, as you have liked bringing up, the Harry Potter population ratios: They are integrated into society, and remember, the prologue tells us they were practically worshiped.
'Wow' III: Based on your reply below, which I will respond to here: you've gone about this the wrong way.
From section 1 on Mistborn, we can conclude an Allomancer (or, depending on when/where the character is from, a Feruchemist) is special, but only in the HP Wizard sense. Twinborn are rather more so, more like Special, but arguably (given the state of Scadriel by the time of Alloy) in the sense of the lead PCs of HP.
However, Mistborn are Special Snowflakes.
From section 2, we can conclude Radiants are Super Special Snowflakes. No, really.
All that said? I cannot in good conscience say "Ahahaha no uberoverpowered" off the top, not least because I've had at least one agent on that scale. (Well, theoreticallyI do: I have a bad habit of not writing. Oopsherpderp.) It is easily possible to write an agent with remarkable powers and special backstory, and possible powers to go with it--Makari's Samuel, for instance, or the even more obvious Dafydd. In the former case, this was nicely underplayed; in the latter, he paid for it hard in spades by the end. It can be done. It just takes care.
However--and this is the big 'however'--for those two (as with most of the best Agents we've had) having the powers wasn't the reason to construct a character, it was part of character development. Your problem is that you're thinking the powers explicitly for the sheer sake of Being Specially Awesome. Remember the original Agents were just plain human.
Referencing the thread below to which I first responded: you said you were thinking only in terms of 'personality traits,' but actually it was SingingTheThunder who suggested personality traits. You did not. You asked for ideas for personalities for two characters with powers. That advice you took, and then back-pedaled asking for powers for a personality someone else had suggested. You hadn't even thought of it yourself. Even that idea, of 'a slightly cracked Mistborn who forgets about his powers' is still focusing on the Allomancy, not on the Agent.
This is not a good way to construct any character, Agent, fic, or original work. You can make those overpowered characters work--I'd still say hold off on the Radiant, too little information and too high a status in Roshar's mythology--but don't think about the powers. Think about what kind of person would be interesting to read about, what kind of person would be entertaining to challenge and make jokes with. Either the powers will come naturally or they won't.
The right touch could manage it. As you're currently approaching it, I would caution against doing so.
(A brief appendix: Dude, you just hopped on board. Kick back, relax, get to know us and learn better how we work--and how our style writing works and how our Agents click. Making Agents comes in a little while. Don't think about it now. Let ideas bubble, let them brew, let them steep into a richer solution. Let the excitement ease up into something slightly less volatile.)