I am physically located in Northern California, United States; not in the core Bay Area but on the coast north of there. When I look up the host that would be fielding my requests on ipinfo.io, I see it is in San Jose, CA. This should be reasonably fast; at least it should not be an order of magnitude slower than, say, Debian apt updates. But in fact, it is 
Every monthly flatpak update is torture, multiple hours for sure. Any guess what’s up?
As a bonus question, if I can’t fix this, can I somehow download the updates in the background on a home server and then apply them on the desktop when ready? I should be able to install the flatpak client on the server, but the problem is communicating the state.
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Ian
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This would need a verbose log from your side, as connections vary from everywhere in the world. And GitHub · Where software is built would likely be the correct place to post them.
FWIW I’ve noticed the same. I’m in midwest USA and have a symmetric 1Gbps fiber connection, and flathub is consistently very slow. Typically killing and restarting flatpak install gives a decent chance of apparently hitting a faster mirror.
On the low end I’ll see 50KB/s (400Kbps) and if I get lucky, restarting the install process will give up to 50MB/s (400Mbps). That is a variance of 3 orders of magnitude!
The remote URL I’m using is https://dl.flathub.org/repo/, which resolves to a Fastly IP address. Presumably there are multiple mirrors configured as origins behind the Fastly service, and sometimes it picks a very slow one? Perhaps those slow mirrors should be removed until they can provide adequate service?
This is all guess work without logs
Distros usually offer a way to use a particular mirror, even if by default they connect to a CDN. Can flatpak do the same? I guess I feel that the limited control I have over the downloads adds to the frustration from the slowness 
If you’re not willing to provide actual logs, let’s start with the flatpak version?