I don't believe that Flynn is actually a villain, we just don't know what the whole story is yet. We know next to nothing about Rittenhouse yet so we don't know what their end game is or how and why Flynn is going to stop them. Can't wait to find out more, this is by far the best show to air in a long time in my opinion! :)

I think his motivation will probably be less black and white, even if it turns out that he is trying to do something for the ultimate good. Already, he is having to kill people and do bad things to achieve his goal. This is true of almost all of our "heroes" of history though. I believe he *thinks* he is good. As to what his connection to Lucy is, we know now that he is not her father (at least her Mom said her father was someone else). I think Lucy is close to him and may be his spouse or love interest. We know she works with him on the time travel project, he has her journal, and he always looks like he admires her and likes her, but that she frustrates him a lot. I'm usually wrong about these kinds of things though, so we will see. I do have a theory about how Lucy's father fits into all of this though...

We can eliminate Father since we know that her father is Benjamin Cahill (aka the Rittenhouse guy) as we saw in episode 6 "The Watergate Tape", we can also eliminate son since in the episode "Space Race" his mother was revealed and was not Lucy, and finally husband just doesn't seem right so that's my reply.

I agree that Flynn is not a villain like we see in the James Bond movies all crazy like evil. I think he is more like a Magneto type villain where Yes he might be working towards a greater good (at least that is what he believes) but his “end justifies the means” attitude doesn’t always sit right with people. Lucy being one those people. I hope Lucy doesn’t have any relationship with Flynn besides he being the antagonist to her protagonist. I’m Lucy/Wyatt shipper personally.