You have to be slightly careful with the term "sub-domain" as some cPanel providers/customers seem to think this is different to the rest of the world; I've seen it used interchangably with a cPanel add-on domain.
So on the assumption that you understand "sub-domain" to mean the same as me, which is something in the form of subdomain.domain.com...
There's nothing stopping you from having completely different and unrelated content on subdomain.domain.com compared to domain.com.
The obvious (potential) disadvantage is that visitors may not remember the correct format and may attempt to visit your site without inserting . between subdomain and domain: for example, if you have bc.com and create subdomain a.bc.com they may instead visit abc.com which would obviously get them something a little different
Another potential disadvantage is lack of (or complicated) email and other peripherals associated with your subdomain; the control panel may not enable you to create mailboxes for a.bc.com (e.g. you@a.bc.com) which may pose a problem for you.
I don't know of any specific dislike of subdomains from a search engine's point of view - www.domain.com is a subdomain anyway, although this may be treated as a special case. I'd suggest that you should ask this part of your query over in one of the Search Engine Talk forums
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