I know that the popular theory is Simon Pietrovich. It's possible, but...I dunno. This is a guy who never appeared on-screen (on-page?), has only been mentioned a bare handful of times, and yet is supposed to be a major big baddie? Seems like it would be a fairly big deus ex machina, and Jim doesn't tend to go in for those IMO. So I have another theory.

What if Cowl is the original Merlin?

note: all mentions of Merlin below are in reference to the original individual, not the current officeholder or title

We don't have a ton of /facts/ about Cowl to work from, but let's review what we do know.

• His magic is incredibly strong.
  Harry comments that Cowl hit him harder than Justin, Ebenezer, Lea, and Aurora. We've been told numerous times that there's only a couple dozen wizards with more raw force than Harry. Merlin, however, was probably one of the strongest wizards around back in the day, and if he's been floating around for a couple dozen lifetimes, imagine how much power he could have accumulated.
• He appears to have inside information on the Council. 
  Cowl comments that he knows the Wardens are nervous about Harry. Merlin supposedly won the Edinburgh complex from a Sidhe lord in a bet; what if he bugged it way back when? I mean, I'm guessing the guy who laid down most of the initial wards and such could probably figure out a way to keep an eye/ear on things. And Cowl says that the Council "isn't what it was." That almost sounds like someone who is disappointed...like, why aren't you living up to the example I set? Or even bitter, explaining his willingness to tear down the Council...
• According to Kumori, Cowl has "a certain measure of respect" for Harry. And on several occasions, Cowl has let Harry off lightly, all things considered; even tried to arrange things to avoid fighting. 
  The journals in Ebenezer's office draw something of a line (dotted, perhaps, but it's there) between Harry and the original Merlin. Maybe bloodline, maybe just the connection between master and apprentices. Either way, Merlin/Cowl would likely be aware of this, and might prefer not to simply kill Harry and be done.
• A certain knife. 
  The first time we saw Cowl (although we weren't introduced then) was at Bianca's party. Where he handed off a knife, or athame. Specifically, the athame that had once belonged to Morgan le Fay. Can you think of anyone more likely to have that around than Merlin?

Those are the facts that come to mind. A few more thoughts/ideas:

• We know from the creation of Demonreach that Merlin time traveled, despite the rules he wrote. So maybe he's been skipping his way forward, thus partially explaining the long life?
• Kumori, and according to her, Cowl, aren't actually looking to do great evil; they want to 'end death' and believe themselves to be working for the betterment of humanity. That...sounds somewhat like Camelot? I can see Merlin justifying lots of behavior with those goals. He (probably) watched his protege Arthur die...maybe his goal is to end death, so that great achievements like Camelot/round table/etc aren't lost needlessly?
• The name Cowl. This one is really a reach, but in lots of stories, Merlin was a druid, and druids have often been (incorrectly, it turns out) depicted similarly to monks, wearing a cowl.
• The voice. It's described very similarly to the Fomor voice we learn about later on. And the Fomor are described as "exiles from myth and legend." That seems a pretty apt description for Merlin, no? So maybe he hooked up with the Fomor at some point and was given some body mods, or something. This could also play into the long life thing. Also, the Fomor come out of Celtic mythology...hell, maybe Merlin founded the group.
• Kemmler. We don't know with any certainty (I think?) what Cowl's relationship to Kemmler was. He is expressed as having disdain for K's apprentices, although it's implied that he was among them at one point. Maybe Merlin hung out with Kemmler for a while in an attempt to learn more about necromancy? And Cowl claimed to be doing the Darkhallow more to prevent the power from going to another than for personal gain: "I intend to take power," Cowl said. "I regard myself as the least of the possible evils." My intuition is that Merlin was the kind of guy who did a lot of things for personal gain, under the guise of 'taking this burden' onto himself.

So, yeah. It's obviously not conclusive or anything, but the math adds up to me.

Where does this leave us with Kumori? No real idea. There's apparently a WoJ that her identity will break Harry's heart, but I can't find the source for that. But the best theory I have is that it's Margaret, Harry's mom. We know she wandered the Nevernever to an insane degree, so if Merlin/Cowl was hiding out somewhere, they may have run into each other. Plus she was nicknamed 'le fay'; maybe he was curious about someone who basically shared a name with his old nemesis? So she dies, he resurrects her, and she joins up.

And one more idea, just because. What if the English dude in Demonreach is Mordred? Maybe...Morgana fucked around and opened a gateway to Outside, using the athame, letting in Nemesis. It corrupts Mordred, thereby bringing about the downfall of Camelot. Merlin imprisons Mordred in an attempt to cure him, similar to Mab's approach.

Okay...now tell me why I'm wrong!