Yeah, my husband and I have talked about that with each other (ie making better use of Lucy's journal). In a "real life" situation, the team would want all the intell from that journal, and it would be more realistic that Flynn would discuss in depth with Lucy. Doubtless the writers would use some sort of plot device that future Lucy told Flynn not to really discuss with anyone, even her, for "timey wimey" reasons. Or something like that.

The sleeper agents are also plot devices, and i agree, seem rather unlikely. The plot device of fate has a way of "course correcting" (which was depicted in both the finale and the earlier Salem episode), and thus the big historical situations that Rittenhouse wants to change, would probably still happen in the timeline(s), although perhaps with different people pushing them forward, rather than the original people Rittenhouse "took out".

I think Rittenhouse needs to be explained a bit more - they seem a rather vague group, with their family bloodlines, etc. Surely there's more folks from the original Rittenhouse line than just Lucy and her relatives.
For that matter, are there higher ups in the organization above Emma and her "new" ally, Jessica? It would be more realistic that Carol and Nicholas were just part of the Rittenhouse machine, not the only big shots.