For the login, I'm guessing you're talking about persisting logins over multiple visits? If so, please tell them to read  http://www.dotnetnuke.com/Community/Blogs/tabid/825/EntryID/1784/Default.aspx which will show them how to set the values they want.

As for the banner at the top, I can see that that is in a text/html module - this allows them to specify any html i.e. just like when you created this forum post you had a word-like interface to add and format text and upload images, so there should be no impediment to them uploading alternative images or changing the html.

As for the navigation, that's simply a personal preference/settings item - there are quite a few alternative menus , most of which offer horizontal/veritical options, fading, full colour conttrol etc. I'm afraid theres nothing technical stopping them from changing the look & feel,the problem (for you) is convincing them to make the changes, not that it's impossible to make the changes. If you take a look at http://www.dotnetnuke.com/Community/ShowcaseSites/tabid/541/Default.aspx you'll see lots of dotnetnuke sites with often very different look & feel.

Cathal