My first 50 was a Juggernaut, Immortal spec. I will be honest I hated using Quinn. I used Vette until I got Jaesa. I got her early on as my girlfriend helped me to complete Chapter 1 by level 25. I used her exclusively from that point on. I never used anyone else and my tank companions didn't see the light of day other than the companion conversations. I have never had any issues until the final fight on my Jugg and then I had to switch to Quinn. Other than that if I had issues I would just make sure I had my stims and hit my interrupts. I will freely admit that I had to hit my defensive cd's but thats what they are there for. It was never hard though. I did all my quests when they were yellow excpet for Chapter 1 which I mentioned above as most of those were red to me. The tank companions are actually a fairly big waste for a Juggernaut as you effectively cut your DPS down to uselessness. Having two health bars doesn't matter as much when you can not carve half of the opponent's health bar before you are both dead. If you are playing a Juggernaut DPSer then its a bit different. Depending on the DPS of the mob you are fighting your tank companion might not last that long anyways.
Now as to disparities, I do not see them like you do. I have levelled a Merc to 50 and while I could do decent DPS I was surprised at how immobile the Arsenal spec is. I used Mako throughout the entire run 1 - 50. SHe kept me alive for the most part and there were multiple times that H2's that I ended up having to heal myself up as well to make it through, whereas my Jugg could just beat his way through fairly easily. I have several other AC's north of 30 and none of them were as easy as my Jugg except my Guardian Jedi though I went DPS with him.
Anyway you look at it, to me its more a matter of personal play style than a class disparity. But then thats just my perception.