Yes,nothing says good father like smoking over the head of a child
And again, smoking wasn't considered bad in the 1800s. You can't uses 20th century standards on 19th century, characters. Things were different. Women also drank lots of wine while pregnant back in older days.
Another example. The age of consent for sex was 13 back in those time. If a 30-year-old man wanted to sleep with or marry a 13-year-old girl, it happened.
You ought to see what passed for "baby bottles" back in those days.
Or how primitive things were to the point that newborn babies had a very high death rate.
This lady smoked around him while caring for him when he was sick.
She always had a cigarette in her mouth.
This Golem smokes around him.
His likes in the character info include smoking, Cross, and girls.
Ultimately, it sounds like you're nitpicking.
And far as Cross' fatherhood goes, he's decent considering he
Cleans Allen's dirty clothes
Gives him baths
Feeds him
Sits by his bedside when he's sick
Worries about him
Offers to stay with him before he disappears
And he's heart-broken when Allen says he wants to keep fighting (and suffering) in the war, instead of resting peacefully.
And Cross has earned Allen's love. Allen was in shock when he thought Cross was dead.
He looks mortified when he sees the blood in Cross' room.
He doesn't take kindly to the Inspector lounging in the room his master was attacked in.
And he's furious when said Inspector accuses him of killing his master.
He is in a frenzy when he actually sees visions of his master's attack
He's furious when faced with the man who he believes murdered his master.
Apocryphos
That's the same kind of rage he shows toward The Earl, who tricked Allen into turning Mana -his original father figure, into an Akuma
Now Apocyphos attacks his second one.
And when he sees Cross again, he says he's happy he got to see him again, even if he's an illusion
And Tim loves Cross enough to lay in his blood when he's gone.
So Cross is not a bad human being. If he were, the author wouldn't go out of her way to show, or mention, other characters actually caring about him.