I prefer the current small button layout over the proposed version with big tool bars, too. While it could look nice, there isn't much often used functionality to put there. Most of the controls happen with the landscape/buildings directly, different from other games who have e.g. unit controls in their tool bar. So I would prefer to keep the visible area of the terrain as big as possible. If the only reason for the bigger bar is visual cohesion than I think a small tool bar, not much higher/bigger than the buttons, should be enough.
The dropup menus are nice, though. It is always so much work to go through the statistics-menu just to open the statistics for a short glance. Maybe even automatically open the drop-up menus when the cursors hovers over them? But it might well be that this will become annoying.
I like the idea of integrating the objectives with the message window. Is there even a reason to create a new category for them? Since its possible to filter for "scenario" messages I would have added objectives as simple messages. Probably the "status" column could be extended with "todo" / "done" options for objectives. Or maybe change the title of the message when done.
And since we are talking about the menus already: Is there a reason why the ingame "main menu" is so empty? In other games there are options like "new game", "load" or the regular options menu which I am missing in Widelands.