It looks like there might need to be two versions of the Ultimate Superman II, one that stands alone and one that ties into Superman Returns. That shouldn't be a problem though with SII being such a ripe ground for fan edits. I don't see the time reversal as being an opiton in either version though. Unless someone can concoct a better solution based on the materials we have to work with, this is the way I see endings:
-If you don't want to consider SR, and want the best stand alone story for S:TM and SII, Lois keeps the secrect, with the last Lois and Clark scene being on the balcony.
-If you DO want to consider SR, the SuperKiss erases her memory of Clark=Superman. One alteration to this would be the deletion of Lois' line "What's happening in the world?" as to suggest she only forgets Clark's secret, not the entirety of the last few days. Surely Perry would ask her to write a story on the events, and she'd definitely think something was up if she couldn't remember any of it. (That's my interpretation, anyway.)

And I don't think Lara should be incorporated. Yes it was a nice idea for Superman to be able to talk to both of his parents, but that's just not the way it was supposed to be. Jor-El already has a larger role here than he ever did in any other incarnation of Superman, and to include Lara on top of that would take away the impact of Superman truly being the last of of his kind, isolated, and alone. Add to that the SII Lara in her crystalline box and distorted voice doesn't mesh well with the rest of the Fortress.