You're right—Microsoft's step-by-step upgrade path (2011 → 2013 → 2015 → 2016) ensures structural integrity, but it's not always ideal. A clean install followed by data migration can work well, especially if you're looking to streamline your system. However, writing custom SQL scripts is risky with complex custom entities and workflows.

Instead, consider using dedicated migration tools or services that handle data mapping and transformation securely. Regarding editions—Dynamics 365 On-Premises is the evolved version of CRM 2016 with modular apps and subscription-based licensing, whereas CRM 2016 is a one-time license with limited future support.

If you need expert help with data migration or CRM setup, check out Outright Systems. They specialize in CRM solutions and can help ensure a smooth transition.