The new system allows you to complete the quest through PVE kills. But it also encourages invader kills.
And I disagree with your assessment of prioritizing Invaders. If I have 13 motes, I’m running from the Invader. Losing a firefight means a significant loss for my team. I’ll let people with less motes deal with him.
And in that way, the new quest doesn’t penalize you for prioritizing winning the match. It’s literally much better designed. Allowing you to complete the quest while also contributing to the whole match.
With the old system it’s like that guy that prioritizes kills in control. So they end the match with 30 kills and a 3+ k/d but no captures. Sure, they killed a lot of enemies, but your team had trouble holding 2 control points and he could have helped with that. Because he didn’t, his points weren’t worth as much. Your whole team’s kills weren’t worth as much. And you lost because of it.
I disagree with you assessments of both the quest and control. I always hunt the invader because I would rather loose the fight and allow my allies to pick him off while he is wounded than hide and let them die. Also, if I stay back in control and hold 1 zone while having a 3+ k/d, I think that I have done significantly more for my team than the guy who charges at another zone and feeds the enemies points. It is easier for a skilled team to win with 1 zone.