My biggest irritation on the Alien Hunters/Shen's Last Gift integration was that there was effectively no in-game explanation. I had done Shen's prior to WotC so I was mostly expecting that, instead, zilch. Just make sparks from the start. So when I did encounter the rulers, Central telling me they were made by Vahlen came from left field entirely. No lead up, no advanced briefing just 'There! It's one of Vahlen's escaped experiments!" I spent a moment just blinking in confusion. Then attacking and getting annoyed with their mechanics.