I'd prefer Bethany...though movie Pepper is ok.
Yeah I see no issue with Stark having a child with his true love, starting a family (allowing for Iron Kids stories) and maybe adopting the baby like you said he delivered in his bad days...she could be the adopted older sister. Original unique characters that have a reason for being and eventually taking over...a Stark family would be possibly VERY awesome.
Then THE Stark could come calling. Lots of possibly family ties...even perhaps children he didn't know he had who are angry he wasn't there for them...even though he never knew they existed.
All better than regressing Tony like Bendis did for a cheap replacement and some terrible attempt at a cool super spy rock n roll mommie. Because Maria wasn't kool enough right...I mean Tony only ever thinks about how he misses her every day right?
THE Stark....as in the alien race from the Guardians? Could be interesting, he was taken to their future once but was returned the instant he left so his memories should not exist of that adventure.
Still what does everyone else think? Should Tony in the comics start a family after this adoption junk is removed?