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Most of the SEO suggestions (great quality content, long form content, engagement rate/time on the page, authority inbound links ) apply to content oriented site.

But what should you do if you are an aggregator or a resource directory?  You aim is to send the user faster to other site they are looking for or provide ranking about the resources. In fact at a very basic level you are competing for search engine traffic because they are doing same things. You may have done a hand crafted, human created resource that is better than what algorithms are showing.  And your site  likely to have lot more outgoing links than content. You know you are better (or getting better) since repeat visitors keep coming back.

So in these days of Search engines, what a resource directory or aggregator site do to rank? Because even directories need first time visitors till they start coming back again.

At a fundamental level, you are keeping the data somewhere and it is rendered correctly. In a CMS this data is stored in a database completely outside search engine view. So it does not matter if it is in database or in physical directory somehow. So there is no benefit in keeping the structure same physically.

Having said that and my own experience (we manage website with millions of pages) managing this using HTACCESS script is NOT a good idea. You will be limited by what you can do and maintaining will be quite challenging.

I strongly suggest consider moving to a CMS (like drupal) and store all you content inside a database and the CMS script takes care of HTACCESS plus gives other goodies. There are several tool available to get your content from disk into a database.

In my experience links shared on google+ are indexed quite fast (less than 10 days)

1. It depends on how the content on secondary domains organized. If each secondary domain has a content theme, then it would be easier to get separate links for each of them and thus it benefits everyone. It helps user to quickly find/contribute what they are looking for, helps to attract different specific links and pass the value to primary.  If there is no such theme, then all those secondary domain will compete with each other  for mindshare, user contribution and attracting individual links which would make them to achieve high DA,

2. I have similar setup. but instead of separate domains I have multiple subdomains with content categorized by theme. It helps may ways 1) Easier for single sign on. Use logged in one site does not need to log in again on anotyher site. 2) Can attract different types of links 3) easier for segmentation for advertisers.  Not all subdomains can achieve same DA or traffic but it helps overall network by internal linking.