In practice, putting SSDs into 3.5" drive bays is a big hassle
When I talked about how we failed at making all our servers have SSD system disks, I briefly talked about how one issue was that SSDs are not necessarily easily compatible with 3.5" drive bays. If you have never encountered this issue, you may be scratching your head, because basic spacers to let you put 2.5" drives (SSDs included) into 3.5" drive bays are widely available and generally dirt cheap. Sure, you have to screw some extra things on your SSDs, but unless you're working at a much bigger scale than we are, this doesn't really matter.
The problem is that this doesn't always work in servers, depending on how their drive bays work. The fundamental issue is that a 3.5" SATA HD has its power and SATA connectors at the bottom left edge of the drive, as does a 2.5" SSD, and a simple set of spacers can't position the SSD so that both the connectors and the screw holes line up where they need to be. In servers where you manually insert the SATA and power cables and the provided cables are long enough, you can stretch things to make simple spacers work. In servers with exact-length cables or with hot-swap bays that you slide drives into (either with or without carriers), simple spacers don't work and you need much more expensive sleds (such as IcyDock's).
(Sleds are not very expensive in small quantities, but if you're looking at giving a bunch of servers dual SSD system disks and you're planning to use inexpensive SSDs, adding a $15 part to each disk adds up fast.)
We sort of knew about this issue when we started, but we thought it wasn't going to be a big deal. We were wrong. It adds cost and just as important, it adds friction; it's an extra part to figure out, to qualify, to stock, and to reorder when you start running low. You can't just grab a SSD or two and stick them in a random server, even if you have the SSDs; you have to figure out what you need to get the SSDs mounted, perhaps see if you have one or two sleds left, and so on and so forth.
The upshot of all of this is that we're now highly motivated to get 2.5" drive bays in our next set of basic 1U servers, at least for servers with only two drive bays. As a pleasant side benefit, this would basically give us no choice but to use SSDs in these servers, since we don't have any random old 2.5" HDs and we're unlikely to buy new 2.5" HDs.
(Sadly, this issue is basically forced by the constraints of 3.5" and 2.5" HDs. The power and SATA connectors are at the edge of each because that's where the circuit board goes, and it goes on the outside of the drive in order to leave as much space as possible for the platters, the motors, and so on.)