Yeah, I cannot get behind the idea of further fracturing the content available to individual characters by actually limiting what Vigilantes and Rogues can participate in. I will reiterate, we're talking about a player base of no more than 700 individual accounts logging in (how few actual human players is that actually, I wonder, given the number of multi-boxers?). If I divide 700 by the 168 hours in a week we get 4.16 accounts logged in at any particular hour. So, it's possible to have all four characters online under this system of further separating the Alignments be ineligible to do one another's content.
Of course, the server population is not evenly spread around the globe; but, even being on the west coast of the US makes the regular I Trials (the only I Trials run on the server, as far as I know) difficult for anyone working a 9-5, especially if they have a commute. The Monday and Tuesday 6pm Pacific start times would be a no go for me if I had to drive. On the other end of things, if I log in on a weeknight at 10 pm my time the thin roster of players is often skeletal, since 'prime time' has passed for those in the Central Time Zone and further east. I can only imagine that it's more challenging for the European and Asian players.
Setting aside the idea of making four little kiddie pools for people to play in, the bulk of your idea is pie in the sky, as far as I'm concerned. I can't imagine the amount of labor required to rework all four alignments, as well as gating off content, and adding moral decision points (both public and private) to every affected mission. Just writing all the flavor text and dialog could be a months long project, let alone actually getting down to the brass tacks of coding such a thing.
I would also like to address your false assumption that being a Vigilante is necessarily any kind of advantage. Many times I log on there are fewer than 10 people on red-side. If I'm playing a Vigilante the only things I can initiate (as far as I know... and please... correct me if there are other things a Vig/Rog can initiate on the other side) are paper missions, tip mission, and AE missions. That's it... all of which I could just do blue-side.
For a Rogue, of course, the situation is better because of the general popularity of blue-side (a dynamic that is a hold-over from Live and is also the case on Homecoming, which has a MUCH larger player base than Rebirth does).
Lastly, I would suggest that your character having a hidden alignment of some kind is something you can imagine all on your own. I've invented all sorts of stories about odd things that played out in missions, things that struck me funny or weird, or from a comment someone else made. You have the power to make your character into a subversive, a patriot, or whatever you want without someone else's arbitrary system telling you what your character is. I'd also suggest that any such elaborate system of twin alignments may aid your role-playing, but it may also worsen other player's experiences. Every new system (and one as sweeping and complicated as you're proposing would certainly be) comes with all sorts of consequences to existing systems, often times of the unforeseen or unintentional variety. I see no way for people to avoid/ignore the changes you suggest, if they don't care for them.
My suggestion is simple and straight-forward and fits with the topic of what to do in regard to the Alignment Merits, and until someone tells me that my idea is a technical dead end (and I freely admit that it may well be), it's practical, it's simple, and anyone who doesn't want to participate in it can just keep their heroes blue-side and their villains red-side. Every weeknight Villains, Heroes, Rogues, and Vigilantes get together for I Trials and I've never seen anyone comment on the mixing of alignments being a problem. Same with ITF, TinPex, yadda, yadda, yadda.
If you just don't like people being able to easily play together, that's fine (personally, I think that's weird, but we all have different tastes).
However, presenting this incredibly elaborate system of twin alignments (I had to read it twice, and I'm still unsure exactly how it would function) as some sort of subjective 'perfect' that would prevent anything 'good' from happening in the years required to implement such a system is puzzling to me.