To easily plot these you would need to append the data into one column. Is there any possibility of generating the data differently so you can more easily append the data?
For example, if you have each x y set of data saved in individual CSV files where the column headings would be the same, but each file name would identify the data. If so, you can import all the data at once by dragging and dropping all the files at once onto the column list. Then each x-y pair would be in its own group.
By then placing all the groups in a higher level group, you can use the gear menu on the highest group to append all the data at once.
That creates the appended set of data that can be plotted with one Points command, where you can have the color of the point vary.
Otherwise, you would need individual Points command for each one x,y column and the colors would have to be set individually.