In a typical MMO there is a progression of quest difficulty, which ranges from simple solo-able quests, to harder group quests, to raid quests, which are generally the most difficult. Companion characters would be a massive help in solo quests, but when you get in a group situation is when things get tricky. In a group that would mean double the people to heal, and more micromanaging for players. If anyone has ever done a simple instance you know that if one thing goes wrong in a pull everyone can get screwed. The same goes for raids: the more people and NPCs the harder it is to coordinate during a big boss fight.
Companion characters could not only have an effect on PvE but on PvP as well. If each companion is different with different abilities, it seems that Bioware would have a lot more work on balancing.
Bringing in companion characters isnt all a bad thing; they bring a whole new level of depth and meaning to your story. If you kill the captain, not only will his family hate you, but your companion could be horrified at your actions and leave you forever.
So whats your view on companion characters? Should they be there for the whole game, or only for leveling? Or they should be there for PvE, and not for PvP?