I too switched from multiple stuff sacks to using just one big pack liner ('contractors bag' rated 2 mil) — and never looked back. The advantages over using different compartments or different stuff sacks are many:
1. More space efficient — I had to actually try this out to convince myself, but it really is true. I can pack noticeably more without using stuff sacks / compression sacks!
2. More time efficient — imagine not having to wrestle your sleeping bag, pad, clothing, etc. into their respective stuff sacks! Yep, just line your pack and then shove everything in. You will soon develop a system that's fast, efficient, and orderly.
3. More weight efficient — every ounce counts, right? Why use multiple stuff sacks if they add weight, and actually waste both time and space?
Tent stuff sack aside (more on that below) — I now use only one small stuff sack to house the iddy biddy stuff.
But what about exposing everything to the rain?
Firstly, I always attach my tent to the outside of my pack. I can thus easily set up tent without opening up my pack at all. And when striking camp in the rain, I pack and close up everything under the protection of my tent — then I just put on my rain jacket, take down and attach the tent to my backpack, and hit the trail. Also, no worries about packing a wet/muddy tent into my backpack.
Secondly, IMO, using a sturdy liner actually provides better water protection! I close up the liner by twisting the end real tight and then bending it down like a shepherd's hook (pointing to the ground) — and then I close and tighten all straps — keeping everything in its place. If canoeing, I add a rubber band to make sure the twists stay tight.
Some packs work better than others…. but I really think using separate stuff sacks for tent, pad, food, clothing, etc. is actually counter productive.