I'd like to quickly respond to some of your questions:
In my opinion, yes CRM is PERFECT for SMB and non-profits.
For # 1 where you said Easily creating customized templates. In Quotewerks, we have a very simple editing interface that's quite similar to modifying reports, but it is built-in versus requiring the use of a separate reporting creation/editing tool.
MY ANSWER: You can make use of advance finds. As long as your query is no more than three dimensions deep, you can use advanced finds all day long to display data and you never need to touch SSRS or another reporting package.
For # 2. where you said "The reports we've modified, don't work. There's no log of why they don't work, there's no error messages, they just don't work. Again, a partner could probably help here, but it seems like this is one of those things that Microsoft could offer without the need to hire a 3rd party?"
MY ANSWER: Are you querying the filtered_view as opposed to the database tables? That's key.
For # 3. Simply emailing a quote to a customer directly from CRM. All the data is there, why do we need to do a mail merge in Word?
MY ANSWER: You can email quotes directly from within CRM. Make sure you configure the CRM email router component to work with your exchange environment, via the CRM Email Router Configurator, and you can easily send email directly from within CRM and even receive email into CRM for automated processing and passing to sales folks if you like.
For # 4.Portals. Wow, So we have to pay $6000 extra a year just to have a support portal? Our Freshdesk subscription is $1500/year.
MY ANSWER: Yes -- if you want external folks to be able to get data or put data into CRM from a portal, then yes you need the internet connector license which allows for that.
I've done tons of Dynamics CRM implementations to the point where rolling them out is fast and easy.
It's the "smallest" Dynamics Product, making it great for SMB. The other Dynamics Products are much larger and have more moving parts, with added layers of complexity. Those other ones are better for larger organizations. Dynamics CRM can scale very large, but it can also work very well small.
Hope all that was helpful!