EMDs can be tricky because they represent a class of domain used by a lot of people for the purpose of promoting niche sites (aka spamming the results). This has been a way many people have made a lot of money - by (1) doing the spamming and (2) by promoting the system. The undeniable fact is that a lot of trashy sites have polluted the search results because of the EMD issue, and Google have tried to exclude them.
The problem lies in a set of key indicators which play out at varying levels and varying combinations in different niches, making it hard to predict what will and won't trigger a penalty - usually the -950 or end of results penalty, less often a penalty of NOT showing the index page but only subpages around positions 100 - 200, and less often still showing the index page around 500 - 600.
The key indicators are:
1) exact match domain name = bluewidgets.com
2) links in using the exact match keywords = blue widgets (and close variations thereof)
3) links in using wwww.bluewidgetsdotcom as the anchor text - this and 2 above can generate anchor text "over optimization" penalties
4) use of a blog for the site structure
5) meta title of "home" page tightly focuses on blue widgets
6) title of blog focuses on blue widgets
7) seo on each post focuses on blue widgets
8) H1 headings on posts focus on blue widgets
9) Keyword density > 1% (I think)
You can get away with having all of these only by chance, and it will be impossible to analyze why you are ranking, since other sites with apparently the same factors will have tanked.
But to be sure of ranking, it is necessary to avoid too many of 1, 2, 5, 6, 7, 8 - the mystery is always how much is too much.
I believe you can have no more than any 3 items out of 5 6 7 and 8 if you are to stand any chance of ranking. And no doubt there are exceptions.
I think the final blow for the EMD crew has been what looks suspiciously like a downgrading of wordpress based sites, or at least a change in how they are assessed.
No matter how good Google's intentions, trying to exclude the EMD spammer crew will cause a lot of legitimate sites (you decide what those are) to suffer.
I too have moved content from EMD to established sites to form new pages on those established sites and they have immediately shown up where I would expect them to.
Additionally, Google have actively intervened to turn up the criteria of trust and authority for ranking in many areas where spammers where prevalent.