I also don't delete... I put troublesome elements in a bak directory, which makes it easy to restore as well as find the maps I've changed.
The reasons:
1) Flashes. Most maps with the warning I have no problem with (I'm not epileptic)... but a handful hit me pretty hard with nausea and disorientation, which can still be effecting me an hour later. After it happened the first time I've become more proactive with removing flash images from maps at the first sign that they might effect me.
2) Can't easily see some or all of the approach circles (because if I didn't want to see them, I'd turn on Hidden). On some maps, it's because of the circles themselves... thin or partially transparent. A lot of the time it's because of one or two combo groups which blend too well with the background... sometimes its pastels on pastels, but a lot of the time it's a dark colour (typically near black grey, purple, or blue) on a dark background. A lot of the time I put up with it, but I really hate it. If there were controls to alter combo colours in the game, probably be using them a lot.
3) Things I think are just pointless... like replacing the combo break sound with a silent one.
Most other annoying stuff I put up with.
I will also admit that I have been tempted to do what others have suggested like replacing videos... either with higher quality ones, or with different videos (like replacing some of the Bad Apple videos for other versions just for variety). Similarly, there are a number of maps that use the same background (or no background)... I've been tempted to change some of those.
