The major criticism was the main content area was too wide (if viewing full screen on a computer), making the text hard to read (the eye has a long way to jump left and right) and too may different things without anything specifically drawing the eye. Also, the flexible column width approach doesn't work too well. If you resize the browser window width the navigation"dots" under the main slideshow all go wrong and seem to display multiple times (on Chrome). [Aside - the navigation dots would be more useful if they had a tooltip giving the subject of the item - might be easier said than done depending on how it has been implemented]
Personally I prefer to stay with fixed column widths, with collapsible borders; I know in some circumstances scale-able content is maybe better for mobile devices, but, unless the columns are excessively wide, most mobiles will display them reasonably well. We often then find some extra graphic content/background to fill the margins - e.g. see
http://www.phuket-pride.org/
But, the main design criticism of the home page is it's too cluttered and nothing draws the eye. Sometimes less is more..... Whilst the headings are all low key and the colours relaxing, its hard to know what the focal point is. Bolder headings would work better in our opinion, along with a cleaner design. Also, the current design, now with two side bars, makes the central column/content more readable as it's narrower, exacerbates the cluttered aspect leaving one thinking "where do I start?" One approach would be to put some of the sidebar items like recent posts into another slideshow, so they take up less space.
Regarding SEO we use a free plugin from yoast that works very well and gives lots of options for setting and evaluating the potential performance of every individual item.
http://yoast.com/wordpress/seo/ Needs a little bit of understanding and setting up but the results are worthwhile.
Hope the above is useful - it's intended to be helpful rather than critical! I continue to wish you well with the project and will give you more feedback when I have time.