Why are so few SSD 3.5 inches?

I think it comes from a handful of factors:

• Demand. For the last few years, laptops have been outselling desktops. Want to make a product appeal to the largest possible audience? Make it work with a laptop.
• Compatibility. Since mounting kit adapters exist and are relatively inexpensive, making the drives 2.5" allows for the most users.
• Many new desktop and server case designs have at least 1 native 2.5" drive mount. In some cases it's to allow for SSD usage, in others it's simply a matter of density -- you can fit quite a few more 2.5" drives in the same space as 3.5" drives. You see this more in server cases than desktop cases though.
• Physical Space. Part of the reason that 3.5" hard drives still exist (besides inertia) is that they allow for larger platters, which allow for higher capacity drives. A large enough SSD to require a 3.5" design would be prohibitively expensive.
• Manufacturing. It costs less to build 1 enclosure design than it does 2.

There's probably a few other things, but those all come to mind off the top of my head.

Finally, since an SSD doesn't have any moving parts, it's not prone to moving around inside a desktop system. Unless your system uses a tool-less mounting system that requires 3.5" SATA drives with the power and data connectors in the appropriate place (e.g. Mac Pro, Dell OptiPlexes, etc.), you can just use a piece of velcro, a plastic wire tie, double-sided tape, or any other solution you can think of to keep the drive from moving very far.

For the few desktop systems I deploy that have SSDs, I just leave the drive sitting at the bottom of the case if there's no other way to mount them properly. It's far cheaper than buying additional kit just to mount them "nicely". Those systems have plenty of thermal headroom such that heat simply isn't an issue.