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My opinions on the answers.
1.
A key element your going to find that overides lore and story is what i call game mechanics versus rp. The matrix itself was a completely digitized version of the world as represented in the first movie when referencing Morpheus as an international terrorist, with websites that featured him in differing languages and differing countires and locations. However to create a game space environment that actually has continents so large and vast it feels like the planet, we'd have to have blizzard backing us - and by that i mean more people playing mxo. The year set in mega city to the generally agreed upon standard is that it is the year 1999 - add on the three years the game has been running if you think that even the blue pill world moves forward so you are looking at 1999-2002. So yes essentially we could go anywhere, but there are limitations in this medium.
2.
You risk walking into a dangerously philosophical realm where in which most answers remain to be seen, but for the most part, the RSI is defined not by belief but rather physical perception - outside of just your sense of space and self which would define your body size, but also truths beyond conceptions like your hair style, or the shape of your hair, the color of your eyes. Different additions can be made, as it can be argued that if we should change our appearence in the matrix, then they become our digital avatars and as such we freely can manipulate them as seperate entities. That being said it would really depend on the individual. For example a patron of RP here (endlessvoid) - his charachters RP is that he has no eyes, as in in the real his eyes would be gone, in the matrix, the digitization of his rsi places eyes in his head, but they are completely black - void of substance - no pun intended. Also scars that you recieved and are wary of would be present on your structure in the matrix.
But then again - we are what we 'know' we are, if one should be dimented, disturbed ect. - and their beliefs about themselves are amiss, one wonders if they would still be animated normally, of if the system would indulge their mental diss-array. But focussing, essentially yes, as long as you know what you look like, and can feel yourself phsyically as in aging - your rsi will also show those signs. A key note to remember though is that it isn't you in the matrix. But i'll stop here before i go on about legs not being necessary to walk.
3.
Well the transistion to redpill from bluepill is essentially a small representation of a journey to truth and enlightenment - but at the same time it comes to mean different things to different people, that's defined by the individual and their story. However the problem with relating to the bluepills that you once knew in your former life is that you have to explain where you've been and what's happened to you. The problem with this is that the general concept is that when one frees themselves of the matrix, their bluepill self either crumples on sight or dissapears completely.
In the case of one Michael Popper- he'd have to explain to his friends and family how he died but wasn't really dead. For them to bury him as they did, his mind would transcend his digital form thus the husk of his bluepill life is no more, and he is granted a new avatar upon comming back to the matrix. (The kid - leader of EPN). But a lot of this would truly depend on the individual in question, and the circumstances behind their awakening. The interaction with blue pills is defined by their own intelligence and abilities, and more then likely made easier by anyone who becomes self-aware or rather self substantiation. Also with the lack of truce in place, your knowledge of the truth could make you a threat to those bluepills and many might try and stop you from dealing with them by any means necessary thus completely causing more damage then helping.
4.
It would depend on the situation behind the bluepill, but one must figure if the machines control our lives like essentially they do, when one battery falls out of placel, they fill it with another. When you know too much you become a risk, it was different with the truce as those who wanted out were 'allowed' to leave, but now with the war back on, essentially things should be the same, the moment you begin to know too much the 'government' will come after you as a means of either silencing you or getting back at the ones who are trying to show you the truth behind the matrix. But questions like these are subjective to cases really, and i think the best way to look at it is the redpill is a personal journey, in that regard, it affects everyone differently. And since we write our own charachters, go nuts since no ones going to complain about you being able to go back to work as a redpill when we have vampires, immortals, demons, god modders, munchkins and so much other fun stuff. 
5. Subjective based on people as always, but if you want a general idea this is what i think works for it:
Zion - Currently working on security of new zion, their goals are to continue to wage war with the machines with a deeper desire for total human freedom, but while looking to keep their security high they will also do what it takes to get an upper hand against the machines and merovingians.
Machine - Essentially they want complete control of humanity for the sake of peace, they want to keep us under control so that things run more smoothly for all of us and the war can stop, however their cold and effecient ways are highly dissagreeable to many, the same could be said about zions pro-humanity views.
Merv - As always the ones who enjoy the fruits of the matrix and do what they need to do to not only protect their way of life but enrich it fully - by any means necessary. Information is power, and power is what they want.
EPN - Rebuilding old zion as it's a holy place in their eyes, they want to awaken those trapped within the system to aid zion in their war with the machines, they are a splinter org of zion so with the exception of event prizes they freely work together. *chuckle.*
CYPH - A splinter org of the machines they desire to protect and save the bluepills of the matrix by preventing them from being awakened, and harmed by all. Though the leadership they recieve from cryptos keeps this is mind, the actions of veil aren't always so representative of the 'cypherite pro-blue pill' way.
That's orgs in a general perspective though, the people and factions behind those orgs are individuals and define their own views and actions, subjectivity is the name of the game.
6.
Can't say i know much 'Abaddon', but the generally accepted RP placing is that there are outposts in the real in place for the machinists and merovingians or that the machinists are still plugged into the matrix - though this would completely upset faction and crew mechanics - but that's my opinion. Also with the ability to transgress themselves as exiles into 'shells' in the real it's completely possible. The general had a base in the matrix known as stalingrad but it was 'destroyed' by the machines? Attacked all the same, cleared out of his recruits.
7.
Depends on RP, always will. Before there were two zions, outside of the outpost business i referenced in 6, an accepted view was that there were so many people in zion that the loyalty of all of it's people would be impossible to determine. As in it would be easy to go un-noticed in the walls of zion, and unless you've been 'awakened' by the machines or self-substantiated, my opinion is that we all end up in zion and go our own routes from there, but that had to change when outposts were set up for machines and merovingians now that they too can preform awakenings, though why machinists would is beyond me. Also if a merovingian hovercraft showed up in zion, if they knew of it's alliance the goal would be to more then likely aprehend it's passengers as traitors to humanity and arrest them.
8.
EJP - Emergency Jackout Protocol
A small addition to the technology of ones neural jack in port that essentially makes you jack out or rather jack back to the loading area to prevent death from occuring to the person in the real. Death as a side effect to death has been reduced to the 'death effect' - a debuff that runs on your rsi for i believe 5 minutes post suffering the traumatic experience of death in the matrix.
This of course is a game mechanic over rp because if you make an mmo where the charachter you work so hard on dies for good when it dies people would tear their hair out and eventually stop playing.
Phew, that was a work out, and no doubt someone just beat me to replying in this post so it's not really been a good use of my time. Hope this helped.
~Darminian
Emergency Jackout Protocol, developed by the late Danielle Wright. The program initiates your jackout routines when your body is near death. Essentially when you "die" in the Matrix, you've only reached the borderline created by the EJP.
