I used to use a bit of both. I'm pretty much 100% squared up now. I dropped the side stance for a few reasons...
It exposes my back and kidneys too much. When people use it against me, I noticed it's far easier to circle to their back side when I counter, leaving them pretty much defenseless if I get there quickly enough.
Because the stance is longer, it's easier to sweep someone in it by kicking out the front leg.
The reverse side hand and foot are a lot further away, taking those a bit too long to reach their target.
What sealed the deal for me is that I've been hitting a heavy bag 3-4 days a week for the last 3 months straight (New Years resolution to lose weight, get faster and stronger still in effect). I'm a lot weaker with my front side, especially out of that stance, and it takes too long to hit with the same power from my back side as a squared up stance.
I'm not saying this is true of everyone; maybe I'm the exception. I've tried to make it better, but it's like fitting a square peg into a round hole. The only application I see for it for me personally is point fighting where power doesn't mean much, and speed of making first contact is everything. Having zero interest in point fighting, I've stopped using it almost completely. I'll find myself in it once in a while through the course of sparring, but it's more of a transition during movement than anything else.
I'll practice it a bit on the heavy bag for if I'm ever forced into it in a SD situation, but I'm not giving it any more attention than that.
Everyone's different. Use what works for you. A lot of things changed for me when I started hitting the bag on a regular basis. And I'm not doing cardio kickboxing on the bag by any means. Combinations at full speed and power, footwork and sharpening basics are what my workouts on the bag consist of, not Billy Blanks Tae Bo stuff.