Hi
Firstly, we would not touch .net for web development. It is as inflexible and modular as it gets and Microsoft and Website are 2 words that should be kept well apart in programming terms.
Open source is more flexible, hosting less of an issue and performance is enhanced. Likewise client is not tied in to Microsoft, licensing etc.
To Magento: you asked what issues we have seen - Performance is horrible. Changing a single attribute to a product in the backend takes an average of about a minute to perform, on an otherwise responsive server. AJAX or not, that is absolutely unacceptable. The frontend, despite being cached, is not all that much better. Yes, you are talking about a lot of features here but at the expense of performance to an annoying degree. The latest version is supposed to address certain performance issues, so well keep you posted if that situation changes.
2.Understand. That while some modules have been created by excellent Magento developers, the vast majority have not. Also keep in mind that any module you install to your website has the potential to cause a problem. This may be a major problem that completely breaks your store, or it may be a minor problem that doesnt isnt apparent at first, in which case it may be difficult to track down the cause.
These are 2 of many issues, but this said it is certainly better than OSC (not difficult). Years ago we worked with OSC, then moved to ZenCart and now OpenCart. That said, these are all in need of reconfiguration and greater stress testing than the out of the box versions give. As with anything free or open source you cannot expect perfection so my Team and I normally redesign, redevelop and build new modules for any online shopping experience we create.
Hope that helps.
Chris.