To me the choice is easy if you consider your user base. If your users will all have Office 365 accounts and Power BI user licences, then use the Power BI service because there is no requirement for custom development. Things just work "out of the box" as they say.
If your users will not have Office 365 accounts and/or Power BI licenses, you cannot use PowerBI.com so you must use Power BI Embedded. When you use PowerBI Embedded, Microsoft charges you per report session instead of charging you in terms of user licenses. This Power BI Embedded approach does require custom development as you must build a custom website to host your reports and dashboard tiles which are embedded on pages using various development techniques.
Note that you can embed reports into a custom application whether you are using PowerBI.com or Power BI embedded. It's just that this custom development approach is optional with PowerBI.com and a requirement with Power BI Emdedded. Note that embedding reports in a custom application provides you with more flexibility in your ability to create a user experience for filtering data, navigating between report pages and making the report with a interactive experience.
