Ok, so I have a few theories about Regina, Serum Queen, and their relationship as created by the Serum. I wanted to throw them out there for debate and see what everyone thinks, plus hear what everyone else thinks is going on. Beware, long post incoming!
Theory 1: On the Origins of Evil
Jekyll's Serum isn't black and white, in my mind. It doesn't just separate good from evil in a person, for a couple reasons. First off, Jekyll originally wanted this serum to excise the "animalistic" parts of a person, i.e. passion and love and hatred and all those powerful emotions, leaving cold and rational man behind. Those emotions aren't necessarily evil, now, are they? Secondly, there's that whole scene in Strange Case(I think) where Hyde walks into the party with Rumplestiltskin, and looks in the mirror and realizes he doesn't look like Jekyll ("the same man"). Rumple responds that that's because he isn't really a man at all, rather parts of one- the parts Jekyll wanted to hide. That's, of course, how Hyde got his name in Once. Now that's given us both some very strong evidence to say that the serum doesn't merely split "evil," and an interesting philosophical question: who decides what is evil? The answer is: it depends on your point of view. Each individual has their own sense of right and wrong. So, in a way, the serum /does/ actually remove evil, but since the definition of "evil" varies by person, and the serum is just a potion and obviously can't conduct a worldwide poll to determine the global consensus on the definiton of Evil, the only thing it can go on is what the person it is injected into believes. Jekyll thought that passion and love and hate were evil- they caused strife, and impeded progress. So, the serum removed those from Jekyll. That's also a sound explanation for why Jekyll still was able to attempt murder after his split- his cold, calculating side was not what he deemed Evil and so it remained with him. So now, we get to Regina. Her Evil was the person she used to be- hateful, lonely, and a whirlwind of destructive impulses being acted on. It also aligned with her dark side, because when the serum was injected that's what she hated about herself. That, therefore, is what was removed. It isn't truly accurate to call Regina the "orignal self" and Serum Queen the "evil self" because that implies two things: one, that Regina- the light half- was the majority of her soul. In reality, I think most of us can agree that darkness and light are in balance within us and its just that one half is more in control at any given moment than the other. The identification of Regina as being the "orignal" implies that her darkness was just a small fraction of her soul, and as we've seen from her backstory, we know Regina's dark side is far more substantial than that. Second, as I've discussed, IDing Serum Queen as the "evil self" isn't accurate either, since "evil" is relative. We know, right from the moment Regina rips out Serum Queen's heart, that Serum Queen isn't fully inhuman- her heart, though darker than Regina's, was not fully black. We do know that Serum Queen is without a conscience, and devoid of empathy, because of her actions and because of what Lana has said. However, that's just because Regina didn't see her conscience or her empathy as Evil when the serum took effect. Serum Queen, though, has some humanity and that humanity gives her the ability to love, as with Henry, and what makes her who she is- her passion and dark impulses are governed by human emotions and are indeed the majority of her being since she's made up of what Regina wanted gone.
Ok, theory 1 is done! Don't let me add to it or it'll be even more of an essay! If you want more theories or have questions or criticism I'd love to hear all of it so just respond! I have several more ideas but I don't want to put them all here since that would end up being much more way too long than it already is. Honestly, my theories are only this long because no one I know irl wants to hear them as none of them watch Once so I have a lot of time to theorycraft in my own head.