That's a very good point.   Thinking in those terms, I'd have to say that Lisa's characterisation in the latest seasons is actually closer to the "classic" early seasons than it was in the Scully era.   In the early days (and I'm thinking up to season 7 or maybe 8) Lisa was always a very complex and often conflicting character.   This (to me at least) made her the most interesting, likeable and believable character.   Then unfortunately she morphed into a very one dimensional parody of her former self (along with the rest of the family).   Personally, I think this was a greater disservice to her character than either the cake scene or the RO, because she lost so much depth and humanity.
By exploring the flaws in Lisa's character the writers seem to be trying to restore some of it's complexity and depth.   OK, in my opinion they're going about it in a pretty clumsy way, without the subtlety and intelligence that was used in the past but it's still an interesting development.   I really must check out some of the recent eps.