I try to reserve the toys with small pieces for when my youngest is taking her nap. Or...I have my older daughter play with those toys at the dining room table where my yongest can't reach.
They share a room which is limited in space so for us gates and seperate play areas are not feasable. But it would be nice!!! I keep the toys they can both use out in their toy bins and the others stay high up in the closet where neither of them can reach them.
Sometimes...depending on the toy I don't even open it. I have a few stored in the closet for future use. Also...if the pieces aren't depended upon in order to play with the toy I will put them away or toss 'em...depending on what they are.
Hope you find a great solution that works for you!