If you use SSD and a second drive, you will forever be moving things from one drive to the other. Fusion does that automatically. And it actually moves _bits of files_ when they are needed or not. For example, when I open iTunes, it displays the artwork of all music files. Fusion will manage to put all that artwork which is _inside_ your music files onto the fast SSD portion, leaving the rest on the slower drive (unless it is music that you play a lot, or your SSD drive would be empty otherwise).
Also, buying a Thunderbolt external drive is pointless. USB 3 drives are just as fast and a lot lot lot cheaper. An external hard drive is limited by the speed of the drive itself, not by the speed of the connection.
So much conveniently skimmed over here.
To start with SSD gives the best PERFORMANCE for boot drives and not these Fusion things. If your SSD fails, you can be up and running from a clone in a fraction of the time compared to a Fusion. Both reasons why professionals are not using Fusion's — hence why the Apple certainly would never offer such a Fusion option for them in their new Mac Pro.
You also do not need to "forever be moving files from one drive to another", you just need to set-up the your Docs, Music, and Video files to always save to the external — a piece of cake.
As for Thunderbolt not mattering over USB 3, that's not really true either. As many people who use both realise; Thunderbolt offers much lower LATENCY. Even on smaller 1/2-drive externals, this means better performance for regular saving/reading to/from an external drive. And as for price, yes USB 3 are more prevalent (just due to Win usage) so there may be more offerings out there, but there are some great deals on smaller Tbolt drives now to make their usage more realistic (e.g. the Lacie 3TB is on sale today, but normally deals can be found), and even more so if you go for higher storage capacity models...
e.g. the WD 8TB Tbolt can be had for £470 = £58/tera. Not bad at all, plenty of space over two drives making possible to use in RAID 1 to offer some level of redundancy*, giving 4TB of space to use over a period of time, depending on your usage could be 2-3 years, making it great value LONGTERM over small cheaper options (WD fixed the sw recently too). And manufacturer guarantees on drive failure are generally good these days too.
*Though not complete redundancy, as for that you'd need a
separate drive, and for the truly secure, preferably with another separate drive offsite, lol! But for someone on a tight budget, RAID 1 is a start.