rocket - IMO, with the New Game + ending, I would think/hope that you could re-use your character with the ending you chose.....Provided they shortly after re-organize the council in whatever way is needed. It'd add some great depth.
Merely because you'd have 3 different openings, depending on what you chose.
fooflexible, you have 4 end-game choices to finish the game with....Heavy spoliers BTW.
#1. Paragon - You signal the Alliance fleet to protect the council's ship that's getting near destroyed by the Geth.
#2. Neutral - You signal the Alliance fleet to focus on the Soverign/Reaper ship, stating that it has to be destroyed as the first priority.
#3. Renegade - You signal to the alliance fleet (which can't contact the alliance vessels, but sent a distress signal to the citadel/you for help) to ignore the Council ship.
Chosing option #1 saves the current council. For the thanks, humans are added to the council.
Chosing #2 or #3 ends with the council (and the largest Asari dreadnaught) being obliterated. After this happens, you, as the uber-specter, get to decide who leads the Citadel in the future. Choosing the human ambassador (whos a complete jerk, as he screws you over near the end) ends up with him choosing a new council of the 3 alien races + humans.
Or, you can choose Capt. Anderson (the only cool human in the game) to lead the Citadel races, as the aliens are so scared of the Reapers, and feel humans are the only spieces to rally the universe against the reapers. I chose this, as Anderson risks his life for Normandy and your character, and he promises (since he's one awesome military genius, and former Spectre candidate) to take the fight to the Reapers, and destroy them before they attack, since an obvious Reaper attack would of annihilated Citadel forces....Heck, the Geth attack nearly did them in.