You can start over with a fully upgraded character. Including the skills you picked from companion loyalties.

AFAIK, who survives the final mission depends on loyalty mission but not solely on that. There are quite a few factors, including a character's toughness (which comes into play specifically....
Spoiler Alert, click show to read: 
.....when everyone holds the line, while you go kill the final boss...)
Also say Jack isn't loyal and you choose her for a biotic job during the endgame, she is likely to falter, causing her and maybe one of your teammates to die. It's all quite complicated. Check here -
Link to Suicide missions details on the wiki.