I wanted to run through both missions before making a comment. On the rogue side, I played a TW/RAD brute; on the vigilante side, I played a WP/SS tanker.
Overall
Excellent job. Both had engaging stories, and very different missions. Both were a good length, not too long and not too short.
The cutscenes. Very well implemented, especially on the vigilante mission. They felt much more impactful than the cutscenes Paragon Studios had made.
Both mission had some very unique elements, especially the rogue mission.
Both stories were excellent in communicating the importance of alignment.
The rogue mission had a nice variety of antagonists, while the vigilante mission had a good cohesion of the antagonists.
Criticisms
These aren't game breaking, and the missions are still very worthwhile to do, but some observations.
The second mission of the rogue story was a little bewildering at first. I had problems finding the NPC, and I was confused at first of the appearance of the arch-villain. A waypoint or a clue to the location of the NPC would have been useful, as I thought his location was actually out of bounds. However, it was also a hallmark mission of the storyline. I liked how the arch-villain could change the dynamics of the mission.
I felt the vigilante mission was easier than the rogue mission. Granted, the characters were quite different, but the elite boss at the end of the rogue mission was more difficult than I expected. I don't necessarily think it needs adjustment, just an observation.
Good job to the people who worked on both missions. You vastly exceeded my expectations.