My Shepard was a Spacer, Sole Survivor who is like 95% paragon (gets mad at injustice and racism, but tries to keep it cool mostly)

For background my Shepard was never actually fond of the military. The sole reason he joined the Alliance was to see space (my Shep being a big space nerd) and travel, which it didn't turn out as well as he'd hoped. Also Shepard never had many friends or a romantic partner before the games, which provided his quick bonds with Garrus and Tali. Shepard developed romantic feelings for Tali throughout the chase for Saren.

In the games when Shepard calls Ashley (who died on Virmire) a friend, he is just being professional sounding as he never liked her remotely after a few conversations about her views on non-humans. Same goes for Shepard's religious sounding remarks in ME3, he's just trying to comfort others. Shepard didn't expierance anything while dead and only shares that with close friends and if people asked (seriously why does no one ask in game?). He doesn't want to go on anti-religion crusades, but rather just be kind and respectful. Even though canonly most the galaxy is agnostic or atheist by the time of the games.

I'd also like to imagine Shepard hung out a lot more with certain people while in transit on the Normandy. Mostly Tali and Garrus of course. Games, vids, etc. Also Tali eventually stayed in the captain's quarters part way through ME2 rather than normal crew bunks.

And of course after destroying the Reapers, Shepard and Tali build their house on Rannoch. Also I'd really hope that Javik does help Liara with her book. I have a lot more but these are just the ones that came to mind.