• Google search results lead to AMP pages. When Jailbroken, I can load a userscript that turns this off.
• Random apps have stupid names on my homescreen. Either the name is in all caps, or it's too long and Apple puts a big ellipses in the middle. I can't rename them unless I'm Jailbroken.
• Stock iOS has two separate low-battery alerts, the first of which occurs when there's still a fifth of my battery left! I'm well aware of the red icon at the top of my screen.
• The stock iOS keyboard has a dictation key I always hit accidentally. I can disable it when I'm Jailbroken.
There are many, many, many more examples, these are just off the top of my head. It's been long enough since I set up my Jailbreak that I don't actually remember most of them, but I use a ton of let's-call-them annoyance fixers, and I don't think I could live without them.