Certain chart types are effectively better than other chart types for certain tasks...what you're running into is a fundamental problem of connected scatterplots. So when you you ask about getting something cleaner I'd go back to trying to understand the tasks users are trying to accomplish as they are filtering for more marks because the solution is often not about finding some way to display more marks but instead to find a way to display *fewer* marks that more efficiently help users answer questions with their data.
For example are they trying to review the connected scatterplot patterns for a certain mark or set of marks? In that case a filter (or maybe a Filter Action that pops up another worksheet) might be better than a highlight. Are they trying to get a sense of values or ranking where bars might be better? Maybe they just want a sense of correlation between a set of values, in which case a trend line might be better?