I feel that it's about time I re-edit my first ever post, seeing as I have had a lot more time to think about it, I can confidently say there was a lot more to this theory than I'd originally thought. So, I'm sorry if I repeat myself, but this is going to be a collection of thoughts that I both have and have not previously mentioned.
First things first, there is her semblance. We briefly see her use it when she scares Neo away from Yang. It appears to be the ability to create portals. On it's own, this doesn't mean a lot, but when you add in the fact that it has the same appearance as the glowing red orb in the openings. This red orb/energy thing also seems to be a pretty major antagonist towards RWBY and the gang, In each of the openings it shows their imminent downfall in some way or the other, and so when a character appears, showing great levels of power, as well as using this same power, I can't help but feel that she's going to cause trouble for the good guys.
This orb also is shown to attack RWBY whilst they fend off an army of Grimm. This would imply that Raven could do the exact same thing. In the second opening, it seems to replace the moon, and cause the entire world to crumble away. As this happens, team RWBY seems to glow, and are the one thing that doesn't disappear. All of this could easily be ominous foreshadowing for Raven to be the villain that destroys everything, leaving RWBY as the only hope to beat her. Finally, in the third opening, it is shown again, directly after we see the picture of Raven when she presumably wasn't an evil badass. The orb directly leads on to team RWBY and team JNPR falling from the sky in a very "We're doomed" kind of way. So even if Raven has nothing to do with the orb (which I personally don't think is the case), this orb is still likely to be related to the main threat of the series in some way. It should also be noted that in the third opening, the orb seems to come from Qrow's weapon, which I'll discuss in the next point.
Now, another thing that seems to show her evilness is Adam. Firstly, their appearance and skills. Adam uses iaido, a combat style designed for the katana that involves striking with the same movement that you use to unsheathe you weapon. From what we saw of Raven's style when she attacked Neo, we can assume that she uses the same style. This implies that Adam probably learnt his skills from Raven. Taking into account the fact that it seems like Adam was not trained at any academy, this makes more sense. Additionally, they both use a red bladed katana style weapon (Raven technically uses a nodachi when it fully extends, but meh, they'e the same thing, just one's bigger). In terms of appearance, they both wear a lot of red and black, and in a Shihakusho style. Additionally, Adam has a red rose on his back, a symbol used by Ruby and Summer, both of whom know Raven well. This was also apparently intended by Monty as Adam's original character design did not feature this, showing that they changed it in order to make the two match.
Next is their Grimm masks. From what we've been told, Adam seemed to wear a mask to show how the world had made monsters out of the faunus, yet this doesn't explain why Raven wears one. The only explanations I have is that either she secretly has bunny ears, or that she is in some way linked directly with the Grimm. Seeing as she doesn't seem to have aged since she disappeared, she could well have absorbed some kind of power from the big bad orb, thus giving her immortality and a load of powers we don't even know about.
The reason I suggest that she may have absorbed power, is also because of Adam. Well, Adam, and maybe his family. In a previous post, someone suggested that Adam could be Qrow's son. This got me thinking about the subject, and, well it actually makes quite a lot of sense. They both have a very similar hair style (especially when Qrow moves his hair back), but more importantly, they seem to have very similar semblances. There is a lot pointing towards Qrow's being absorption of energy, and physical attacks. Yang, as his niece, seems to be able to absorb physical attacks, and from the "Black" trailer, it seems that Adam can absorb energy attacks. This definitely points towards Adam being at least related to Qrow. Now, as Raven is Qrow's sister, we can also assume that she has an absorption based semblance as well. This also implies that Qrow could be working with Raven as, well, they're brother and sister. Therefore, it doesn't seem too much of a stretch to say that Raven could have absorbed the darkness that creates the Grimm, or something along those lines. In any case, she may well have absorbed the orb from the openings, and in doing so, become an immortal Grimm/human badass who goes around doing whatever she wants.
Seeing as Adam has a lot in common with Raven, I'm fairly sure that there is a definite link between the two, and if Raven has a link with Adam, whom has been shown to be a vengeful, angry monster, it's safe to say, Raven may not be perfectly good either. If Adam is Qrow's son, (or Raven's as this works too), then it would also add a lot of drama as Yang would be his half sister, and RWBY seems to love drama.
Speaking of Yang - Raven saved her life on the train. Now this may seem to point towards Raven being a heroine and not the villain. However, it is not uncommon for villains to have some slither of good within them, and seeing as Raven used to be praised as a legend when she was part of Qrow's team, she clearly had a lot of compassion. It only makes sense that she would therefore protect her daughter. Fending off Neo was likely to show Neo that she was crossing a line by trying to kill Yang. Although we don't know much about Raven's abilities, it's safe to say that she could have killed Neo if she wanted, yet instead she let her go.
It should also be noted that she saves Yang on a White Fang train. Although she can teleport, it would make sense that Raven knew about the train if she could accurately make a portal into one of its moving carriages perfectly in time to save Yang. This makes me suspicious as to whether or not she just happened to know about a train that have adopted her fashion sense and are lead by a man who seems to be directly linked to her.
This next thought is very far fetched, but I thought I could still put it out there. When Raven first looks at Neo, you see her blink. Now this could be her blinking to show that she was not happy with Neo (which is a common feature in animes), or it could have been there to show that she had red eyes behind the mask as it was quite difficult to tell. However, when she first blinks, you only see one eye close. This could be due to angles, or it could have been Raven subtly winking to Neo to tell her to leave. I know this one's probably not true in the slightest but hey.
Back to Yang. There is something that seems to be too detailed to be a coincidence, and this is Raven's similar appearance to Yang. Not only to they have almost the exact same face shape, but Raven also wears very similar clothes to Yang, save them being more Japanese, and Grimm related. This implies to me that they could quite literally be Yin and Yang. Seeing as Yang has a lot of good, yet also has her moments of cruelty, it could be suggested that Raven is evil, with only moments of good.
Due to the music and visual effects used when Raven removes her mask in front of Yang, I believe that it may not have happened yet, and may later occur in a dream, or during some kind of freeze-time ability that Raven has. This is also shown by the fact that Yang has shown no signs of meeting her long lost mother this season. Raven could be contacting Yang in order to try and convince her to join the bad guys. Yang's eyes turn red when they meet Raven's, this suggests that she is angry with her mother (for good reason). However, it would also be expected that Yang would be at least slightly happy for having her questions answered, instead she seems to look at Raven with rage. This could imply that Raven has just done something terrible, then trapped Yang inside some sort of dream/freeze-time state so that they can talk.
Yang's answered questions also brings me onto my next, albeit quite short point. This is one I didn't think of, but was noticed by another member of the RT site. They pointed out that when Yang went to Raven's cabin, they found Grimm. This could just have been a coincidence, but seeing as Raven seems to have several links to the Grimm, this seemed a bit suspicious. Especially so when Qrow appeared to save them.
As someone who has been searching for and fighting the enemy that "no one knows about", it's hard to imagine that he happened to take a break from this to walk along and find his sister's cabin where his nieces just were wandering to. I personally think that this scene suggests that Raven is the villain, and she had left Grimm in her cabin to stop Qrow, who is hunting her, from catching her.
Finally, I just have some various other comments. Firstly, Qrow suggests that Torchwick was the one head of a King Taijitu (presumably the white one from his attire), and that Cinder was the black head. Just as a thought, what if these Grimm connotations didn't only apply to Torchwick and Cinder, but the other villains as well. If this was the case, then Adam and Raven already have masks to suggest which ones they represent, and Raven's is the Nevermore - something that has been shown to be far more dangerous than a King Taijitu.
Additionally, the music that plays whenever Raven appears isn't exactly what you would call heroic. The use of minor notes, and certain crescendos and jarring notes (ooh look at me with my GCSE music) seems to imply that, well, she's more of an unstoppable force, than a loveable saviour.
One final point. Cinder appears after the end credits of volume one, revealing herself to be the "true villain". Raven also appears after the end credits, but of volume two... Hmm.
Anyway, this was both fun and tiring (I wrote more for this than I do for most school essays). Hopefully it all makes sense. This is probably the most effort I'll put into a post for a while :P
Now all I need to do is wait for Sod's Law to take effect and prove all of this wrong. Even if this does happen though, I think I'll just be happy to know that best gurl is getting more screen time.