The day of all-SSD is coming (and I'm no fan of electro-mechanical devices), but for now it's still budget vs. mass storage needs, day-to-day maintenance, and "weakest link" analysis.
I have a 3TB Fusion in my Late 2013 iMac, and nothing that's happened in the last half-year makes me regret that choice.
First, it's turned out to be incredibly fast. Is it slower than pure SSD? Yes. Is it way faster than HDD-only? Absolutely.
It's low-maintenance. There is no need to actively manage storage locations. No, "Whoops, I forgot to point the new app's data storage to the HDD!"
I'm definitely not convinced that OS and apps are the only thing that benefits from SSD speed. Why shouldn't the data I'm working with actively have a home on the SSD, too? Fusion automates that.
I'm definitely not a fan of the notion of a system that's dependent on an external drive for core functionality. That doesn't matter whether it's SSD inside, HDD outside, or vice versa. OS and apps need data to be of any use, and vice versa. If it's a matter of internal SSD, external network-based data, that's one thing - there's plenty of room for data redundancy, there are several paths for accessing that data (wifi, wired). A locally-connected external drive is dependent upon one cable and a pair of mechanical connections. For backup, for supplemental data, that's fine. But I wouldn't depend on that cable as the sole link to my data. I shouldn't be dead in the water if that link fails.
Any split-component system, whether both components are internal, or one is inside and the other out, has this fundamental weakness. In terms of risk analysis, that cable is far, far more likely to fail than either an HDD or SDD.
Simply stated, keep it all internal, let the computer manage speed optimization. The computer is a tool. The less attention you have to focus on the tool, the more attention you can give to the task, and it's the task that matters.