A better question would be....given what we know exists in this world....and what factions we already have/know if...
If there is a mystery faction/race/whatever pulling strings to antoginise the elves against the Templars...who or what might they be?
Technically it could be almost anyone: we know there are more than nine worlds in the multiverse, and you'd think each world would have at least one faction. The sky's the limit as to what might be out there. I'm not saying aliens are definitely behind everything... but it could totally be aliens!
If we had limit the guesses to something based on what we've seen in game so far, however, the only definite faction we know of are the Hellspawn. They clearly have a motive and we know they're up to something. But we've been assured they can't use magic. That makes is unlikely they could easily fool both factions on their own, which implies they are either pawns or allies for yet another faction. This effectively just reframes the original question, so who's left?
The simplest answer is it's a rogue elf or Templar who teamed up with the Hellspawn to settle some longstanding grudge. That's plausible enough and it would keep the number of factions to a minimum, but it's a little underwhelming. It's not like we've been hearing about some legendary figure of the past who could make a dramatic reveal as the big bad (well, other than the MC's father, but that would require some painful contortions to fit).
There are only two other option I can think (short of pulling something completely new out of the hat). The first would be Fiona's 'family.' They have some level of power, and it would fit in with them pitting the Irish factions against each other for their own amusement - they've taken their games to a larger stage. It would also be an easy way to tie Fiona into the main plot. The downside, though, is that it would feel like quite a coincidence to meet Fiona just before her past catches up with both of us.
The other option is the vaguely defined 'powers that be' who actually enforce the secrecy of Neverwhere on the world. Based on Kaija's speech we know they must exist, and the Templars have to work around them to some degree so they'd have a potential motive to want the Templars gone. But we know so little about this group that they're only the smallest step up from it being a whole new faction.
Put all that together... and IMHO it doesn't point in any particular direction. Not the most insightful analysis I'm afraid, but there you have it.
