I do agree that the sub menus can get crowded fast.
I took the sub menu, and placed it down the left side.
Then made a new class called wrapper in the admin css, which was a direct copy of the .wrap style.
Then took any reference to something like wrap h2, and made it wrap h2, wrapper h2 (etc).
Then, edited the sub menu's css to make it flow down the side, and edited the wrap class to make it accommodate the menu on the left. (I edited wrap for this, since there are more pages with sub menus than not.)
Finally, some pages don't have sub menus, some do. Some can go either way. For the ones that "always" have a sub menu, nothing to do (why I edited wrap class). For the ones that could go either way, like the dashboard, I added a variable in menu-header and set it to false. Then in the call for the sub menu I set that var true. Then for those pages where it's a toss up, I added an if check inside the class="" area (where it said wrap).
I did have to edit the padding on a couple of things, because of an overlap with the post box content and the right menus when on post/add link, etc.
So that helped with the clutter, and keeps a long list of sub-menu tabs from wrapping to a new line and mucking up.
Now for the order, I hadn't really thought about it. For me at least, I prefer to keep them the way it is. This way users that are familiar with WP don't get too confused and can distinguish between WP menus and added plugin menus.