I'm doing the same as you. Trying to replace plants that die off with more native plants and trying to ignore the eye candy. I actually just bought some more native plants for this one bed. I've always had a hard time getting things to grow (including decorative trees) so am switching to natives in there.
I don't have any water features since we're surrounded by creeks and ponds but do have a water bowl for the animals and birds to drink from. Brush piles are in the woods in the front of the yard because our yard slopes to the creek and we were having issues with erosion even with all the trees there. The brush piles have helped with that plus given all the wildlife places to hide out.