That's your opinion, and that's completely fine. I personally like Malgus myself having read his novel and so forth, but I think we can both agree that Malgus by comparison to his boss, was a far more effective villain. You felt his presence and the chill of evil with him throughout the game far more than you did the Emperor, even in the JK class story.
But you hit the nails in the head there my friend
Comapred to the Emepror, yeah, I'll agree that he was more effective as a villain. I think BW:A tried to go with the whole mystery man archetype for the Emperor as a protagonist, and it wound up not working because we simply didn't care two credits about him or what he was trying to do.
Plus Malgus was a poster boy for the Sith, so in the advertising build up to launch, you kind of wanted to know more about him then the Emperor.
And this is why no fans were upset when the news broke that Episodes 7 thru 9 will overwrite this particular part of EU history.
Ironically, doing so does VERY LITTLE on the narrative outside of Anakin Solo's death and Chewie's death, which I'll be the latter getting killed in the movies too, and for EU concerns, Anakin Solo could've died in some other event for all we care. It really doesn't affect too much of the narrative prior to or post. That's pretty sad when a series can alienate itself from its own continuity and when its own creators can look back and ask "*** IS THAT?!"
Wait, really? That's the best news I've heard all week o.O