Is there a way to get the user input to stand out more…when scrolling back up a long list of prompts, outputs and messages the formatting for a response and user input - surrounded by a thin box line - is very similar - a different colour would be useful. or compress all the tedious output?
Does one of the 10,000 Cursor edit settings change this?

There isn’t a dedicated Cursor setting to pick a different color just for your messages vs the assistant in Agent/Chat. Those bubbles follow the overall editor / workbench theme, so the main knob you have today is trying another Color Theme (Command Palette → “Color Theme”) and seeing if contrast feels better.
There also isn’t a single “compress all long agent output” control in settings. For very long threads, splitting work across new chats (and using checkpoints when you want safe rollback points) usually keeps history easier to scan: Agent overview.
This comes up a lot — worth upvoting / adding detail on threads like this one and this one so product sees demand.