Cryptic has been "initiating development on several new projects" in one form or another since at least March 11, 2007. This likely originally included Star Trek and Neverwinter, as well as the repurposing of Marvel Universe. No telling what they've specifically got in the works now, but it's been a standard marketing line for at least six years.
I was hoping someone would do the work for me and use the way back machine to see the date this current "secret project" was listed on thier website. I have a hunch about it and if the timing is right I am Super Surprised. lets just say that.
Editing: Ok I checked the timing and it is dead on PERFECT!!! september 14th 2011
The way back machine shows that prior to this particular 'secret project' there was another secret project, now I actually got lucky because the way back machine only has records dating back to 2011 for this particular page and I needed to see a previous secret project to determine the start of the current secret project.
The old project was for Atari.
the new project is for a nameless company, or at least one that does not want to be named yet.

So what does the timing tell me? the project started somewhere /around/ the beginning of 2012. I.E. about 1 year before CoH was put on closing notice.
infact, just enough time for certain discussions between companies to relay back and forth on what was desired aka finalizing the project details and giving the go-ahead on the plan to commence.
Realizations;
NCSoft knows City of heroes is not marketable to asia. so why would they take the time and resources to develop a sequel in a korean company? simple they wont.
if NCSoft wanted to make a sequel to CoH why would they fire paragon? because paragon was barely able to make additions to the original game, obviously creating a sequel would have been too much for them to handle, they were fired because it could be legally objected by paragon if NCSoft were to seek outside help to develop the sequel rather than resorting to the staff at paragon who were supposed to be in charge of that and had the IP leased to them.
in the business world an IP can only be legally leased to 1 company at a time. I found that out with nintendo, they had a game being developed by a lame duck developer who was doing nothing and squating on the IP, they had thier hands tied and couldn't lease the IP to anyone else till the current lease expired.
Also for many who didn't know this; after some really indepth talks with Aeria games I learned that NCSoft is merely a publisher they have no actual ability to edit/make the games they hire other companies to do that.
yes I'm saying what you think I'm saying; this 'secret project' is actually: CoH 2
I don't know who initiated the contact first, but I'm certain that NCSoft and Cryptic have been talking about creating a CoH 2 for months before we were put on notice, thats right NCSoft is turning to a seasoned developer of MMO's and the creator of CoH inorder to get the sequel made. First they had to discuss all the nitty gritty business formalities which took a few months though the project had been put up on cryptic's page. next they needed to make it official they needed the IP lease back from paragon.
when you take away a lease from a company that subsequently gives them no right to even run the product linked to that lease. in effect Paragon would have been left with nothing to do, twiddling thier thumbs and waiting around. - this is the legal aspect NCSoft claimed required the shut-down of CoH. so rather than keep useless employees on the payroll they fired the whole studio.
but CoH /HAD/ to be shutdown for this to happen.
so now the lease went straight to cryptic, and obviously NCSoft wants to keep it secret to surprise us.
Hence why Cryptic has not released a name of a company they are developing for this time.
When paragon employees approached NCSoft to buy the IP NCSoft would not agree to thier terms. why? cause they felt the lease was safer in Cryptics hands for development purposes. now why not just tell them that? because SOME paragon employees would tell someone, and that someone would leak it to us. then it's not a surprise.
so, yeah, Positron is now working at cryptic and cryptic is working on CoH2
I of coarse have no hard evidence to support this except the timing but I'd say it's a dead ringer.