I think that you are on the right track with your ideas here. I had a similar issue, and I tightened up my home page to basically make a statement about the topic of my site, and then lead to links to the main pages of each sub-section, with a description about each one. As well, I added to the content on each sub-index so that there was no confusion about the specific subject of these pages. This seems to have worked well with whatever changes Jagger I, II, and III have implemented.
It also makes sense for your visitors. Use home page to describe and introduce your site, then provide a description of the different categories or sections available, along with a link to the main page for each section. Reflect the importance of these pages in the navigation for your site - so that each page points to home, plus each main section home page, whether you call them "bluewidgets/index.htm" or "redwidgets.mainpage.htm" or whatever.
Currently, my home page is PR6, and it leads to about 10 sub-section indexes that are all PR5. This is working supremely well for me, with both my homepage and the relevant section page being listed on page one in many very competitive google serps right now...which is where I truly believe that my site belongs, given my observation of the competition. (Ok, I think I should rate ahead of some shady slim-content contenders, but that's another issue.)
Only you know how much worth your site has, and where you feel it belongs in Google serps. Be honest with yourself...but my sense, after reading your post, is for you to go ahead and tighten your home page as I said, and create a theme for your main sub-pages, as you suggested; it seems to me that this will make a lot of sense to Google and will be indexed accordingly.
Tighten up your meta descriptions also, as you alluded to. For me, a site slogan that incorporates a lot of my key words is the main home page page meta, then on main sub-pages, I tighten it further, to include a keyword rich slogan pertinent to that page, almost as if this was a subdomain or a domain of its own.
I could be way off base here, but I don't think so, so I'm offering this advice purely because I owe something back to the ppl of WebmasterWorld who have been so helpful to me.
Apologies for the length of this post.