I use the Patagonia Capilene Cool shirts, both short and long sleeve, and love them. I actually like them better than the older Capilene LW version.
For bottoms, I was in the same boat as you. Was bummed to find out they stopped making the Capilene LW bottoms and that they weren’t going to make Capilene Cool bottoms. Don’t understand that.
So, I tried out the Montbell Zeo-Line LW bottoms. Worked well. Didn’t like them as much as my old Capilene LW bottoms though.
I then tried out Montbell’s new Super Merino LW bottoms. They weigh about the same as the Zeo-Line LW bottoms (approx. 4 oz.), but I like them a lot more. They are very comfortable, insulate well but also breath well when needed, and they don’t hold in the stink nearly as much. They are much more expensive though ($69 vs $34).
If you don’t mind the extra cost, I recommend giving the Montbell Super Merino LW bottoms a try.