I had a similar feeling about PvP in SWTOR. At the moment I have mostly stayed away from it because it definitely reminded me too much of how WOWs PvP was for battlegrounds. It was a bit too frustrating then, when I played WoW, how closely PvE and PvP were tied together and how a change in one affected greatly the other.
Balancing both PvP and PvE at the same time seems like someone is always going to be upset. I think what they should do in SWTOR is take advantage of the companions for PvP. I would suggest a PvP system where players could use any of their companions to play as in the BG for the PvP battles. Each companion could serve different roles so any player could play as the role (Tank, Caster , Melee, Heals) that was needed for each battle that they queued into. It would be even better if before the battle was started a list was shown that allowed each player to make choices on which companion to bring based on what roles had already been chosen via the companions their teammates selected. (Similar to League of Legends Selection Screen before the battle starts where you build a team composition)
The advantages of such a system would be instantaneous balance to the PvP especially if the moves each companion had were limited to only one Quick slot bar (So at max a total of 12 different abilities) as well as homogenized so that every role has essentially the same abilities as every type of role that companion was. Thus Ashara Zavros (Melee) would be similar to Jaesa Willsaam (Melee) but i suppose you could name the abilities different names for uniqueness. It would also separate PvP from PvE which would allow for better PvE balance changes and would probably make it a lot more competitive and fun in a battleground because no one class dominates.
I would still suggest keeping rewards in the form of armor as is currently the way things are, but the armor that would be obtained would be for each of your companions. It would require more of investment to gear out all 5 of your companions ,if you truly were into pvp and so desired, than a single main character would... but might give players something worth grinding several BG's out over and over for. As for how it affected the Players Main Character, maybe make certain Augmented Orange Sets, that have a certain PvP look to them, purchasable in addition to the armor for each companion. This way players would have a look in PvE that represented their accomplishments in PvP. I also think this system would not be to big a stretch in the lore aspect as it is very plausible to consider your character sending off a minion to champion or fight for your cause in a battle.
Anyway love it or leave it thats my suggestion on why you should hold of on Rated BGs and how to fix PvP!
I