I've also been frustrated when testing out tools that kinda keep you locked into one predetermined view, table, or set of tables at a time. I made a semantic data modeling library that puts together queries (and of course joins) for you as it uses a drill-across querying technique, and can also join data across different data sources in a secondary execution layer.
zillion looks fantastic. I've wanted for a long time to build something similar for warehousing the education and social science research data I work with, but have found it difficult to spend time building infrastructure as someone currently spending most of their time in academia. What does your company do, if you don't mind me asking? Any interest in expanding into research data management? I'd love to chat with you sometime if you're at all interested... (my contact is in my profile)
https://github.com/totalhack/zillion
Disclaimer: this project is currently a one man show, though I use it in production at my own company.