Completely agree with you on no.2 - it would have been totally understandable for Lana not to be apalled about Lex and his fotw experiments. The woman spent seasons running away from those guys to the extent that in reality you'd be in a looney bin. Then the conflict, in a sort of Vader/Luke imitation, after her finding out Clark was also a freak so to speak would have been a much better reason for her to have been torn and ultimately pick mr goody two shoes...rather than "actually I've decided this week that I'm not actually in love with you Lex and I don't want a baby with you. Sorry 'bout that, laters!!" like wtf?
Naughty lazy writers *angry face*

On the Lois front I always would have liked Clark to have kept his glasses after the episode where he gets glasses...er...title escapes me.....Anyway and then bring Lois in after that so she wouldn't recognise him later and all that (because I'm a sucker for traditional Lois and Clark) but like you said in hindsight she should only have been a character that popped up now and again maybe. And the hitting over the head with the destiny thing did wear a bit thin shall we say.