I've had my own gripes about my 18-200 giving me soft focus. Now someone says that it is the sharper of the two lenses. Hmmm.
Anyway, in the pic off the two doves, the vertical branch at the right of the pic seems to be sharper than the birds. Perhaps you were focused on the wrong things.
In the pic of the flying geese, the geese seem to be ok, but keep in mind the old bird hunter's adage. When there is a flock, pick one bird to shoot at. Same with auto-focus. Gotta focus on one bird, or better yet, one part of a bird (usually the eye, but with a flying bird that gets a little tricky). Also, considering the pic of the doves, in which there are nearby things, one of which seems to be sharp, you might have a front focus problem. It doesn't show up in the geese pic because there is nothing near the flying birds to be in focus.
In a class on bird photography I attended, the instructor suggested always use continuous fire and track the bird; out of a series from one burst, some will be sharp and others will be less so. This seemed to hold true this past weekend on flocks of snow geese where I was firing 3 to 5 second bursts. (I use 5100 with a 150-500 sigma lens.) Some were hand held (standing up or hanging out of a car window) and some were from a Wimberly head on a Vanguard Auctus 323AT tripod.
And then there is the pixel density. I wonder if anyone has played around with the concept of an optimum pixel density beyond which you have to mount the camera on a 5 ton granite slab. Perhaps this continuous fire would be helpful here. Figure the first shot is a throw away because your trigger finger was moving and the last shot is a throway for the same reason. But the in between shots have a better chance of being sharp because the only motion is tacking the bird.
But hey, these are only random thougts from someone who is also struggling with sharpness issues.