I've had both. Ran the atlas for a few years and the guy that has the boat now still runs it with zero problems. It's a great unit. The only benefit I would say the bobs has is it is much, much faster and smoother operating. I've become accustomed to the operation of the bobs and I used the atlas on my dads boat the other day and had to get used to it again.
All that being said, if weight is an issue get the atlas. Much cheaper too
I have also had both and not only is Bobs much faster it's FAR more reliable. The TH microjacker in prone to breakage due to binding. I know of four people on this forum including myself who have had the Microjacker break. TH is gray about sending you a new one but you have to replace it. More importantly piece of mind comes to mind when 20 miles from a boat ramp. Following is a service bulletin link for the Microjacker that basically says you need to adjust the nuts for tightness every time you use it