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Things That are annoying

Adobe Flash

You know the reasons. Doesn't work on android, proprietary, expensive, etc.

MicroUSB Connectors

Maybe mini USB was even worse but nobody noticed pre-smartphone. Maybe cables from reputable manufacturers are great. But cheap no-name charging cables sure do seem to wear out fast. I liked 3.5mm 5v connectors better.

The exfat filesystem for SDXC cards

Really? using an expensive proprietary standard for the main storage card used by most phones, cameras, computers, and everything else?

Basically every lithium-ion charging algorithm in existence.

If you're smartphone had a setting that gave you ten percent shorter battery life but doubled the lifespan before you needed a new battery you would probably use it. That's what reducing the charging voltage to 4.1 from 4.2 would do. Some laptops have this option but most smartphones do not, and common cheap linear regulators are all 4.2v fixed.

Lithium Ion at all

Were it available, I would totally choose a phone with LiFePo4 batteries that go 2K+ cycles, even if it was heavier and bulkier.

XML Where XML shouldn't be

XML isn't really for simple heirarchial data or lists or most of what you find in a config file. Can't we all just use YAML for config?

Dimmable things that don't dim enough

Screens are often too bright for totally dark adapted eyes, not distracting people when doing tech work in a dark place, etc. Also, sometimes the loudest notch on a volume control is too loud.

Android's new floating action button

Was posting to facebook really difficult before the FAB?

Physical devices that depend on the cloud

Some people want to use things where the internet isn't. Others just don't like buying things that could stop working at any moment if the service shuts down.

I've seen cloud IDEs, cloud PCB layout tools, cloud everything. Why would someone want a piece of software that isn't directly internet related(Like e-mail, off-site backup, etc) to be in the cloud? Where they can discontinue the service, get hacked, increase their prices, change their interface to something bothersome, without even asking anyone?

Misc web design

Endless scrolling usually results in a feeling that you are only one wrong click away from entirely losing your place. It makes it harder to share pages. It sometimes barely works.

Sometimes it isn't that awful. Sometimes there's weird javascript tricks happening that put extra data in the URL to make it sharable and linkable. That makes it a bit better, but still, what if there's a long page of threads and you want to see what was up a few years back?

Reddit has a good balance. Their subreddits have pages, even though the threads have "load more" links. It's pretty well done, and permalinks exist.

Another annoying thing is mobile sites missing basically all the reasons one might go to the site. Like search, full descriptions, etc.