Soul pierce is never getting printed in an environment with good general counterspells

Aren't creatures easier to answer than spells? Negate is a much better spell than Remove Soul.

not in limited ;) Notice how negate and mana leak can coexist, but not mana leak and essence scatter

This isn't in the same limited format as mana leak?

Also you're looking at one situation. They had to cut a counter, they chose one. No matter which they chose, you would be saying you can't print leak with the one they cut. You can't set grand Magic design laws over something that has happened one time, especially if you don't know the reason. It's more likely that they just wanted Negate in the format more than Essence Scatter.