Merging two different domains - subdomain or subfolder?

[SEI]

My company has two sites on different domains. We are considering merging the sites into one and keeping only the dominant domain. The dominate site is already a sub-domain of a larger organization so the new sub-domain would be two levels deep.  I realize this is a little abstract so below is an example

Dominant company site:       company.root-domain.com

Secondary company site:     other-root-domain.com

When they merge, everything will be on company.root-domain.com. Should it be

• other.company.root-domain.com   or
• company.root-domain.com/other

Note: The other site has several hundred pages. Both sites have strong authority and link profiles. I want to maintain as much of the value on the other site as possible with the merge.

[SEI]

Thanks. I didn't think it would make too much of a difference but I wanted to get another opinion. I'm not worried about spammy URLs. Everything will be off of a short .edu - they look pretty clean with multiple subdomains.

[brad.s.knutson]

I personally don't think it would make a difference one way or the other, as long as the proper 301 redirects are put into place and all traffic to the old URLs is sent to the correct new URL.

I do, however, think the sub-directory approach looks cleaner.  Anything beyond the first sub-domain looks spammy to me (or just sloppy).  That's just me though.