First of all, I'd like to say I really enjoy the option to choose paths during the faction quest lines.

Sometimes however, I'll find out I took a near impossible path.

During my play with the Vodyani I got the quest Locus of Lies. It has you search for the Tabernacle. To do so it gives you two options, a scientist option to explore or a militarist one to bring the system under yourcontrol. I choose for the militarist quest, but boy was I wrong. The system I now had to colonize only had one planet, Lava. They only way for me now, to complete this quest, is to somehow get Ecologists elected to pass a law that allows me be colonize it. I've had a similar experience with the first quest with the Sophons. I choose to explore, but got attacked early on. I would have had the other quest completed had I chosen that one instead. And because of the early raids I wasn't able to complete it until later in the game.

Things like these completely halt the faction quest progression. So, maybe an option should be added to allow you to switch to the other quest if you can't complete it. Or maybe both options should simply be active at the same time. Allowing you to work towards both untill you finish one. It wouldn't be that weird for a civilisation to try both options to one problem.