Using subdirectories has no effect on SEO, apart from giving a small clue to the site's organization.
The ID is required in the URL in order to find the correct question. What happens if you have multiple questions with the same title?
Using the ID doesn't adversely affect SEO either so removing it or moving it to the end will have a miniscule (if any) effect on SEO. In fact it's standard practice on most sites nowadays, and sites like Stack Overflow have no SEO problems.
It's not worth the effort.