So this idea came about after a *really* productive brainstorming session on the discord. I'm not even the one who came up with the original suggestion (kudos to Erpmario!) and it still needs a lot of details figured out but I like the overall idea enough I'm posting it here to keep the discussion going and to avoid it getting forgotten on discord. In a nutshell the basic idea is that we take the how alignments work in Praetoria/goldside, and expand that to work throughout the entire game.
So just like in Praetoria, a character would actually have two alignments. The external/public alignment, and an internal/true alignment. At the beginning of the game players would choose their internal/true alignment, just like you currently do when starting in Praetoria. Though unlike Praetoria's binary loyalist/resistance choice players can choose the current 4 hero/vig/rog/vil alignments. As players go through the game they are given moral choices that are affected by, and can change, their public alignment just like happens in Praetoria. Also just like Praetoria, this does *not* change your true alignment. If you're a true hero and turn public vig/rog/villain then like Praetoria certain options open up for doing things a little differently. For example a true hero that is a public villain may have the option to secretly report back to the Freedom Phalanx about what's going on in the rogue isles. Or a true vig but public hero needs to arrange an "accident" when taking out Lord Bloodthirster the Genocider instead of simply executing him like a public vig would.
One big difference though between the current Praetorian system and this new proposed one is that there has to be a way for players to change their true alignment as well. Characters evolve, players come up with different ideas to play existing characters, and eventually there is going to be a point where people are going to want to change the true alignment so that they can continue to go undercover for their new alignment and not forever be stuck only doing undercover work with their initial alignment like with Praetoria. With Praetoria this isn't too bad because it's only the first 20 levels and then it's a non-issue. With this suggestion you will have a true alignment all the way to the end game and it would be bad for people to get "stuck" without being able to grow their character as they want.
Doing this would not only open up a LOT more options with how alignments, swapping sides, and AM's work, but it also give us the possibility of breathing new life into old missions. Now instead of just being a hero rescuing Fusionette yet again as you go through the Faultline arc on your billionth alt. Your public hero could be doing secret stuff *while* rescuing Fusionette in order to arrange smuggling Sands/Nocturne/Castillo (which one determined by your true alignment) into Faultline. Then at the end you have the option to *choose* who you give the PsychoChronoMetron to, either Yin, Sands, Nocturne, or Castillo (with corresponding public alignment change) at the end! Your true villain public hero decides he doesn't care about his cover anymore but also doesn't care enough about Arachnos to give it to Nocturne (villain choice) so you sell it to Sands (rogue choice). Now you're a true villain public rogue because the world sees publicly that you're looking out for yourself and will be treated accordingly. Now imagine lots of little stuff like that throughout all the various arcs in the game. It would be absolutely awesome and glorious.
Now, is this idea very ambitious and going to take a ton of work? Absolutely, there is no way this is going to be RI2 or even RI4, But I'm hopeful that this idea will gain traction as a long term goal and that with a bit of luck we'll see RI7 "Undercover Alignments" for the overall alignment revamp itself and RI8 "Stories Retold" for the mission rewrites.
Edit: A few details to consider and need resolving. What about tips and collecting AM's? I'm personally leaning towards 4 types of AM's, one for each alignment type. AM's are not lost if you change your public or private alignment, however each type of AM can buy things slightly unique to the alignment type (alignment specific signature summons being an obvious choice IMO) and don't convert, or if they do there's a fee. So if you have 7 vig AM's and 1 hero AM then you're still not buying that 8 cost purp until you get 1 more vig AM. I also think you get AM's based on what kind of tips you do as it's representing people treating you based on how they view your actions, regardless of your internal reasons for different actions. Want that vig AM? Better start doing vig tips and publicly start acting like a vig.
Another question is, what, besides alternative side stories in missions, does a players true alignment give them? The public alignment is obvious since the game treats them as that alignment similar to what alignment does now. But what, besides RP reasons, does a person have for being a true hero public villain rather then a true villain public villain? I'll be honest, RP is good enough for me but I feel like there should be some sort of gameplay change around it. Maybe you always keep the alignment power of your true alignment regardless instead of your public alignment? Maybe you can use any saved up signature summons of your true alignment? So if you're a true villain public hero then Captain Mako will be willing to help since he knows where your true loyalties lie, though that may be a little odd on teams if your fellow teammate "hero" turns out to be close pals with Lord Recluse.