I have had a minor issue with compatibility with some of the other components on my sites and the guys from bowthemes have fixed it straight away.
haven't had any bug issues. Support is really good. Opencart modules work well. Upgrade works really well and is seemless.
Some of the negatives are that opencart themes don't work, however Mijosoft have created some themes that can be modified with a little bit of knowledge.
It would be good to have some better themes out of the box though for it.
It is difficult to apply numerous opencart modules. For example if you want to apply products in a category as a module, you can really only do it with one category.
Unless you go through a pretty big exercise of duplicating the opencart modules. If you have a lot of categories it is pretty time consuming.
That is the main area where some of the joomla integration could be improved.