The Queen in AVP was BIGGER than the one in A2.
I know on the collector's DVD the commentary says she is the same size, or 16ft, as the one in Aliens was 16ft, BUT she looked much bigger on screen.
Looking at the one in AVP I got the feeling she was even more T-Rexoid in build, except for having a bigger set of primary arms which a T-Rex obviously did not have. Oddly enough the secondary arms of a queen actually are reminiscent of a T-Rex.
The design changes were more than just giving her a smaller waist to make her more streamline.
A closer look reveals that her legs, which were not shown much in A2 any way, were made much larger on the AVP Queen, and it gives her a sturdier look.
As a general rule of anatomical physics, the larger an animal is, especially a bipedal one, the larger the legs have to be in proportion to the over all size to support its weight.
Example: if your 6ft and 200 pounds, you may only need 40% of your mass in your legs, if you're 20ft and 8000 pounds, your legs would need to be 60% of your mass.
I'm not sure if they considered this when making the Queen for AVP, as that is looking into it pretty far, but looking at her wire frame, made by Stephane Paris, sure enough the legs are proportionally bigger.
Other changes were that the primary arms of the Queen no longer are attached to her back close to her spine, but instead the shoulder inserts on the sides like on a regular humanoid, or the warrior/drone aliens.
When I first watched the movie, I got the impression that the primary arms seemed a little smaller in proportion to the Queen, but again a closer look reveals that it is just the rest of the Queen (aside from her waist) that is bigger.
Even her head, which was made from scratch this time, looked bigger.
Another design change was the adding of the crescent shaped "neck crest" that regular warriors have, that the A2 queen lacked. There were other details I am leaving out of this, but you can see they at least paid respect to the original design, and did not change it so much you cannot recognize it as a Queen.
So now how on earth can "both queens be 16 foot" and one clearly look larger than the previous one?
Simple: the Queen from A2 was 16 foot when standing completely erect. The Queen from AVP was 16'when standing at a 45 degree (or less) angle.
The scene where the AVP Queen stood erect, before she fell through the house sized building; she clearly was taller than it. Well over 16 foot.
So there you have it, the AVP queen was 16 foot, so was the A2 Queen, but only if the A2 queen was standing vertical and the AVP queen was hunched over.
I will add that personally I liked the design change for the Queen. We hardly saw her, and most of the aliens lack a lot of the qualities that we liked from the earlier films, but the AVP Queen did look better IMHO.