For example, if I trade a Bunnelby to Cliff for his Farfetche'd in Santalune City.
No, the in-game trades are preset and will always be the same exact Pokemon traded to you. The gender, nature, characteristic etc are all preset, and thus, I deduce that those Pokemon cannot be shiny.
As for whether or not they are female, some of them will be, if they were already meant to be female. Of all the in-game available Pokemon for trade, those are females:
- Stevie (Eevee) from Elena
- Thumper (Steelix) from Farris
- Ralts from Diantha
The others will be males.