I have done it after using Fusion Drive for a year. The performance improvement on the pure SSD is mind-blowing...
I regret not doing it earlier.
The only issue is that 120GB is limited and must be used wisely. I can't really use bootcamp in SSD with that little space, but I can have a Windows VM in Parallel which I use to work with development apps. It's all blazing fast.
Now I use the 2TB HDD occasionally to store some media, and the 120GB SSD to store all apps and my work VM.
It feels like a new Mac.
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Re: yes, I did a better job than the OS
Here's the thing - if you have a 121 GB SSD in a Fusion drive you have as much Flash storage as many laptop owners live with on a daily basis. If you can do the vast majority of your computing within that 121 GB limit, then "pure SSD" may very well beat Fusion. In essence would it matter whether you had a 128 GB MBA with a 1 TB external HDD, or a classic Mac Pro with a 128 GB SSD on one sled and a 1 TB HDD on another, or an iMac with a split Fusion drive?
"Doing a better job than the OS" may be little more than managing your resources wisely. As someone who codes, you're already more knowledgeable about resource management than the vast majority of end users.
As you admit, living within that limit takes some work. One of the primary premises of Fusion is that there's no work/management required. There certainly is a trade-off with Fusion - performance for convenience and cost.
Fusion was never sold as a high-performance computing solution. It's been sold as a way for typical users to get near-SSD performance on their desktops at near-HDD prices. Users who have been accumulating data over the course of decades, typically doubling the size of their HDD with each new machine in order to have room for further accumulation.
The same users who might never take the time to clean out their old junk are also unlikely to manage a split SSD/HDD configuration to run efficiently. Their User folders will be resident on the boot drive, and even if they've moved their iTunes and/or Photos libraries off to the external, Documents, Desktops, and Downloads are going to keep growing until that 121/128 GB limit is reached and the machine grinds to a halt.
I've said this often, but for the ways I use a computer (which is nothing like the way you use yours), I see little difference in day-to-day performance between my late-2013 Fusion-equipped iMac and my much newer, all-Flash iMac. Most of the time my computers are waiting for me; I spend nearly no time waiting for my computers to do what I've asked. But if I was regularly compiling code and loading VMs... I can see how things might be different.
For specific professional needs, all-Flash, like a beefier CPU or GPU and more RAM, is a justifiable business expense. And professional or not, if someone can easily afford a Mac with 1 TB or more of Flash (even if it's just for the sake of infrequently-accessed data) I'm not going to tell them they're wasting their money. But for the "typical" budget conscious user in need of large amounts of storage? Fusion remains a very viable option.