Hi. My opinion :
1. Running OpenCart independently would definitely be much faster and look better
A little bit faster, OK, maybe, but it doesn't mean too slow. "Look better", globally, no : you have much more Joomla templates than for Opencart, and the Mijoshop or Joocart use the Joomla style for the modules. It's only the product details that need a few custom CSS, sometimes.
2. If you run OpenCart within Joomla, you do not get as much support from the community
Maybe, for some questions. But you have a much faster and professionnel help from the editor of the Opencart integration in Joomla (previouly mentioned).
3. Extensions you get for your OpenCart store would usually not work right out of the box without modifications
Most of them work on Mijoshop, and all of them on Joocart.
4. Extension developers might not give you support priority when you run heavily modified OpenCart within Joomla
As I said : no heavy modification. I just remember a small modification needed in Mijoshop for a payment plugin (Payzen). The editor, Payzen, made it freely.
5. You pay more for a software to put OpenCart within Joomla, while OpenCart is free by itself
The cost is nothing, compared with the service you have, absolutely necessary for professionnal websites. You can't leave a professionnal site with a problem or closed for several days, or weeks, waiting for an answer in a forum. And several paid Opencart extensions are useless in Joomla, because you use the Joomla extensions (SEO, backup, security, galleries ....).
6. You usually don't use Joomla's features after putting OpenCart in
I know very well Joomla, and I can tell you I use a lot of functions in Joomla with Opencart "inside". There is 10 times more extensions for Joomla for a lot of functions (and much more sofisticated) : slideshows, galleries, blogs, forms (for quotes for ex.), forums, editor (JCE), sheduled backups, SEO, security ... and thousands of other extensions to make your e-commerce website much more interesting, secure, and optimised for Google.
7. It's much easier to customise OpenCart itself, than having it within Joomla. It's like having a container in a container
It's always easier to customise the components you know the best. That's why I use Opencart in Joomla : I have all the possibilities of Joomla (and with all the extensions I already paid) + all Opencart.
If you know better Opencart than Joomla, for e-commerce sites, you're right : for most projects, you should use Opencart, and just install all the extensions you need, if you don't want functions needing Joomla.
Sometimes, there is another reason to use Mijoshop or Joocart : you create a site with Joomla for a client, only to present the company, the services, the products, and a few months or years later, he wants to sell his products in line. As you don't want to re-start another site, and as you can't have the same style and so many and nice functions for the presentation of the company in Opencart, you just add Opencart in the site.
This is not a fight to be for or against Opencart in Joomla. It's just my experience of this subject.