I find that having Lois suffering from post partum depression actually explains a lot of things about why Clark isn't stepping up to the plate, so to speak. If the depression wasn't in the way, she might see that she's actively keeping him from properly relating to her.
Yes, he's still fixated on Lana who seems to have gone a little wild after Clark left her, but he also doesn't have anybody in the know who can tell him 'Hey, get over her, you have a life and she's not waiting for you.'
And yes, sometimes it does take parents a while to click with their newborns, and sometimes it never quite happens. (I mean, if the bonding was perfect and instantaneous, I doubt there would be nearly as much infant abuse.)