I just finished reading the book myself and found it quite satisfying. Now I was a fan of Superman before the Crisis on Infinite Earths so I am quite used to the idea of Clark being the disguise to Superman's reality. In fact in the book, Clark holds onto the idea that Lois might still be in love with Superman, not Clark.
Lois barely noticed Clark's absence oh these many years since they weren't partners, nor were they best buddies. She basically welcomes him back in the usual Lois way: "Hi, Clark! I heard about your travels. How were they?" and before he answers, she's rambling about something else completely ignoring him.
As for the smoking thing, the movie is definitely a continuation of Superman II, therefore Lois smokes. In Superman, the Movie, Superman tells her, "You really shouldn't smoke..." In the book, he says exactly the same thing to her in their meeting on top of the Daily Planet. Clark is mindful of what he said last time, so to re-connect, he says exactly the same thing and Lois remembers. Just like Clark in "Barbarians at the Planet" to the guy on the elevator, Superman repeatedly blows out Lois's lighter before making his appearance.
And Lois doesn't actually smoke in the book. She's trying to give it up. At the end, she's tempted to smoke but puts out the lighter herself before Superman drifts down and tells her, "Thank you."
The book constantly refers to Lois's first article, "I Spent the Night With Superman", Perry's statement about associating Superman with the Daily Planet like "death and taxes", "Abbott and Costello", etc., Luthor's obsession with real estate and references to California sliding into the ocean, and numerous other things from SI and SII so it's clear that it's a continuation. Therefore, you can't expect the pre-Crisis Superman to suddenly become the post-Crisis Clark. You would hear screams from Superman fans about inconsistencies with the first two movies.
Be glad Superman III and IV were completely forgotten as if they had never existed. They still don't, at least in my DVD library.
As for Jason, I don't believe Lois knows her son is Superman's son if he really is intended to be. Lois says Jason was born prematurely and almost didn't make it. Lois's memory was wiped, so she doesn't know she slept with Clark. So it's apparent she thinks the boy is Richard's but just premature. That means she started dating Richard not too long after the events of Superman II. Why they made Jason sickly, I have no idea. You wouldn't think that Superman's son would be that way.
As for Jackie's deal-breakers, Lois wasn't expecting trouble when she took Jason with her on the interview. There was no hint ahead of time that a diabolical madman was behind the blackouts. She thought she'd fit in an interview between that and her Pulitzer ceremony so I don't think she thought there would be any danger. She certainly didn't expect to run into Lex Luthor.
Plus the Fortress was never destroyed since it was operational at the end of Superman II. The molecule chamber was certainly still active. The only bit of destruction that was apparent was a blackening of the control panel. The structure was fine. And apparently the green master crystal (oddly was white in the book) revived or re-grew all the other crystals, otherwise there wouldn't have been a control crystal Luthor referred to in SII that would control the molecule chamber.
If there is a sequel that settles the whole Jason matter, I'd be happy to watch both. If they leave it as it is, I'll be unhappy since it leaves so many questions up in the air. Since I enjoyed both incarnations of Superman (pre- and post-Crisis), I expect to watch it when it comes to DVD (Kids make it nearly impossible to watch things in theaters anymore).
Be glad we didn't have Nicholas Cage as Superman, Lex Luthor as another Kryptonian, and Kryptonian powers derived from the suit rather than the yellow sun. That's what the first few scripts had that were eventually trashed.
Oh, and the guy who wrote the book, Marv Wolfman, was formerly chief editor at DC Comics and wrote much of the series, "Crisis on Infinite Earths", so this guy is quite familiar with the DC universe, both pre- and post-crisis.
