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I am seeing from my own research that many times a SE will see a sub domain as a completely independent site if you structure it that way
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That was what I had planned to answer you yesterday as well, but I didn't have time..
Sub domains is, as you say, a good way to organize your site, and by using sub domains you can also place your forum etc. on a separate server (to balance the server load) since you can just point the sub domain to it.
But a (major) disadvantage by using sub domains is the same thing; it's regarded as a separate site..
Search engines do look at the amount of pages you have indexed, and tends to rank sites with lots of content/pages higher than smaller sites.
And by keeping you forum on the same domain (not using a sub domain) you create a lot more pages on your main site and you may rank better because of that.
Another disadvantage by creating a new (sub) domain is that search engines tends to rank older established sites better than new ones, so you may end up in the Google "sandbox" for many months on your newly created sub domain and have to "work your way up" the SERPs.
That may take a long time compared to just creating a new forum folder on your main (established) domain...
Hope this answers your question..