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I say, the shorter url with most popular keywords, related to the on-page content. Links, where are they coming from?..what are their Domain Authority and anchor text when linking to your page? That is where I would focus. Build it healthy, otherwise you are propping your business up on a leg that may get kicked out with a google change..

Also I would check the sitemap to ensure nothing is limiting specific sites from being indexed.

I have some experience with network installation and management using Wordpress CMS. All data from the subdomains is visible to the top level domain. Each site should maintain their own SEO properties, and this can be enhanced by using domain masking applications. Making the subdomain.mysite.com appear as myrealsitename.com

I would say that a properly run network will reduce maintenance overall, eliminate human errors from exploring users, and allow easy network wide installations, manual program inclusion, and platform updates.

But a simple answer, a top-level domain will always be a better bet that a subdomain. A network is best for the network top-level, reduces their work load, gives total control, and fairly simple to setup up. Networks to benefit from the intercommunication capabilities that outside sites would not be able to achieve.