I would say the placing of the custom logo in the header area.
As it stands, there does not seem to be a straight forward way for a user to add their own logo in the css, however, it is simple enough in Themes if they simply add a URL to the logo image they wish to use. It is much simpler to add the URL but sometimes a person wants something a bit more complicated. The logobox and the .centered left and right stuff seems to really be designed for only the ElkArte branded logo. If a user adds their own logo and simply change the name to logo_elk.png then the user logo will appear in the Support Information bar, which should only house the ElkArte logo.
I removed all the .center stuff, added a background image to the header area, made the necessary placement adjustments, removed the logobox stuff in the CSS file and in index.template.php, template_above_body I removed the original logo stuff and removed this.
echo '
<div id="logobox">
<img id="logo" src="', $context['header_logo_url_html_safe'], '" alt="', $context['forum_name'], '" title="', $context['forum_name'], '" />', empty($settings['site_slogan']) ? '' : '
<div id="siteslogan">' . $settings['site_slogan'] . '</div>', '
</div>';
and added this.
// Lets remove the logobox and display only the site slogan. Not the Factory Default.
echo '
<div id="siteslogan">' , $settings['site_slogan'] , '</div>';
Which was a challenge because even though I spent 8 or so years in 'C', I don't know a think about .php.
Keep in mind that I am not a CSS master at all but I can get around with FF and Firebug. Of course, anytime you read someone elses work you have to follow it and try to understand their reasoning. The changes I have made so far I have tested and retested to be certain the header was stable and all other areas functioned properly.
It took me a bit of time to understand the variants theme. Had to figure out how and where they were being called from. Once that was sorted and I understood how varients work, I had a clearer mind as to what to do with the theme. I also discovered that to properly create a theme that does not use the default varients of _light and _besocial!! that you have to remember to change the path in the index.css and index_varient.css files for the images to be found.
edit: first paragraph clarity ... I think.