It looks like you're new here. If you want to get involved, click one of these buttons!
I remember back what SWTOR was in development that things like falling to the dark side and being redeemed where meant to be part of the game. At present the alignment system is only for getting access to certain items depending on your light side or dark side rating. The faction swapping system that existed in City of Heroes could be adapted to SWTOR and would suit well with making a story out of how you came to join a different faction but would require a little expansion on the City of Heroes system to take the players light side or dark side rating and class into account. The way faction swapping worked in City of Heroes is that you had the 2 main factions which were Heroes and Villains, then you also had 2 hybrid sub-factions which were called vigilante and rogue. Sometimes when you defeat an enemy they would drop an item called a tip which could be used to get an alignment mission http://paragonwiki.com/wiki/Alignment_Mission and depending on what you choose to do in the alignment mission you would receive a point of fame related to the faction the fits the choice you made. When you have earn 10 fame for the same faction through alignment missions you would then receive a tip item to start a morality mission http://paragonwiki.com/wiki/Morality_Mission. Depending on what you choose to do in the morality mission you will either change faction to the one you have earned 10 fame in, or reaffirm your alignment with the faction you are already in and gain a buff that last for 1 week real time. Players could not go directly from being a hero to being a villain and if you were in one of those faction you would only get tip items to start missions that would give you the opportunity the become either a vigilante or a rogue. Vigilantes and rogues were able to go to both hero and villain areas and do missions in both, but certain missions that were specifically hero or villain faction only and when it came to joining supergroups (guilds) vigilantes could only join a hero supergroup and rogues could only join a villain supergroup.
Adjustments to make to this system that I think would make it better suit SWTOR are as follows.
1. Change the name of the alignment missions to tip missions and the name of the morality missions to loyalty mission since the primary factions in SWTOR are about major societies in the galaxy and the light side/dark side rating is the players alignment.
2. Have three hybrid sub factions that are aligment based. Separatist (dark side), Deserter "those who leave to get away from the war and fighting" (Light side), outlaw (any). Players would only get tip mission items for separatist missions if they are at least tier 1 dark side and will only get tip mission items for deserter missions if they are at least tier 1 light side.
3. Choices made during tip missions and loyalty missions will also effect a characters light side/dark side rating.
4. Loyalty mission items for the empire faction will only drop if your character is dark side tier 3 or greater. Loyalty mission items for the republic faction will only drop if your character is light side tier 3 or greater. Loyalty mission items for the three hybrid sub factions will not have this restriction.
5. Classes that completely cross over to the opposing faction will count as being the equivalent class in that faction while a member of that faction for the purpose of content, story missions and equipment. i.e. A jedi knight who joind the empire would count as being a sith warrior.
6. The random loyalty missions a player can get will be class specific and also relevant to the hybrid sub faction you are joining/leaving and will provide the reason why the character changed factions. i.e. how it came about that a trooper deserted the republic army or how a smuggler was recruited to work as an imperial agent etc.
7. Players who are members of the republic or the empire can't get tip mission items for the opposing faction but players that are members of any of the three hybrid sub factions can get tip mission items for either major faction and either of the other two hybrid sub factions.
8. A player who is a member of a hybrid sub faction can't get access to any class story missions but can go to any empire or republic area and do the non class mission there. Members of the hybrid sub factions can also get spontaneously attacked by groups that either oppose or prey upon those sub factions. i.e. local law enforcement may recognize an outlaw and attack, pirates may attack deserters and republic troops may attack separatist.
9. Separatist can only join empire guilds and deserters can only join republic guilds. Outlaws can create their own outlaw guilds which can act as either an ally or enemy to republic or empire guilds.