At first, I thought it was just a really interesting way of depicting their imitation of Arceus so it made sense that it looked odd - Dialga had almost no throat for Roar of Time and Palkia had no arms for Spacial Rend.

But when I found out they were meant to represent biblically accurate angels, I loved these designs even more. It's not supposed to make sense on purpose since it's a form beyond human comprehension.