First things first. The comparison of the theme file structure is missleading. There are A LOT more than required templates shown in the WP directory. All you need for WordPress is two, an index file and a style.css.

But what is actually different from WordPress?
Main thing is actually Ghosts requirements and the complexity that comes from that.
The biggest thing thats missing here is that they use nodejs. Which user can easily host and configure that on their own? Wheres the target group that commercial devs are suppose to sell too? Almost no users can use it easily. Nodejs has a lacking support on Windows (mostly 3rd party npms but none the less issues).
And for a hosted service, there are no frizz providers already.

Its cool and so forth but whats the unique selling point for the project?
Nodejs? almost none of the ones that want a no frizz easy blogging system that can be self hosted easily can use it. If its hosted, the end user dont care. Also complex in comparison to get WP running (See http://ghosted.co/install-ghost-digitalocean/ 10 steps are actually like 38 commands or steps)

Markdown? easily added to WordPress if need arises. Its a bummer there is no support for this in core yet though. (The whole blogwriting should really be refactored)

Handlebars for themes? woopydoo. There are easier to use solutions for end users and devs to work with. Jade is such an easy template language. (See http://docs.ghost.org/themes/ my eyes hurt from all the {{...}})

Then there are those that donated and dont get what they expected since the wording and the promotion was somewhat missleading. Can read about it in their support forum.

Easy to develop for? WordPress
Easy to setup and get hosting for? WordPress
Existing ecosystem with lots of good resources to learn from in one owns dev endeavors etc? WordPress

In conclusion, basically what WordPress can learn from Ghost is:
1) Simplify the blog posting, support Markdown.
2) Simplify the admin area

PS
Ghost is just suppose to be a blogging platform, that is, as far as I understand it. eCommerce support and all that jazz seems really to totally go against the whole point of Ghost.