I noticed a ton of inconsistencies with plotlines, as well, I noticed quite a few of the older ones were fucking boring compared to the newer ones. Some of them were broken, others are totally useless. 

So I'm doing three things:
1: Rewriting backstories and storylines to have more consistent connections with other characters.
2: Removing certain characters who are too similar to other characters that I have. 
3: Taking concepts from removed characters and adapting them to other characters.

I'll probably lose 20-30 characters, but the characters that I have left will be better off.