The system's lead conversion process does two things decently well. First, it automatically converts standard types of data for you, such as moving tasks and campaign information from the lead to the contact and opportunity. This means some of your flow might be doing duplicate work that could have been saved by default functionality. Second, it provides some canned reports that include things like lead conversion rates and ROI reports. This also tangentially leads to other benefits if you're using Einstein Scoring systems, such as predicting the win rate of a given opportunity or lead, etc. Your leads won't be properly scored without this lead conversion process, thus resulting in inaccurate data.
If you don't care for all the extra bells and whistles that the canned conversion process provides, then that's fine. You should simply be aware that by eschewing this process, you're losing out on the future potential benefits of reporting and Einstein Analytics. These features may or may not be useful to you in the future, and certainly some random person on the Internet shouldn't presume to know your business model and organization's needs.
That said, perhaps a hybrid approach is warranted. You could perform the conversion as part of the flow in order to preserve future analytics, and use the flow to fill in the gaps that standard functionality doesn't offer. I won't presume to know too much about your current process, but perhaps it could be as simple as a drop-in InvocableMethod that simply performs the actual conversion and maps the account, contact, and opportunity data back in to the flow to finish up the process.
In our org, for comparison, we have a custom lead conversion page (and soon a Lightning Component) that does a lot of custom conversion, but also calls the standard Database.convertLead function. We use Lead Scoring and Opportunity Scoring, though, so that was an important thing for us to implement to get our analytics correct. We use a hybrid approach that I mentioned in the previous paragraph to give us the flexibility we want while retaining all of the benefits of standard conversion.