OK, the drop-down next to the reply button and that button itself are a bit wonky, but I never use them. I think the grouping of the other elements is one of the nicer aspects of Gmail.

Buttons represent actions. Clicking a button mutates the world. Links represent places and views. Clicking a link takes you somewhere or changes the appearance of something.

Links along the left are global. Buttons along the top and bottom of the center panel pertain to the current conversation or selection of conversations (depending on view). Links and buttons on each message operate on, oddly enough, that message.

Maybe Google's general style doesn't meld well with the way you think, but for many (most?) people, it does. It's a fantastic design.