I respectfully think that, for home defense purposes, people are over-thinking the ammunition except for the question of over-penentration.
The typical scenarios for which I prepare are a burglar who happens to be armed or a known-armed home invader He/she is not after me personally, he's after my stuff, and he is not likely to remain downrange to express an opinion on my choice of loads. If he does remain downrange, it will be because he is unable to express opinions on my choice of home defense loads or my marksmanship. Another factor is that I may not be the person doing the shooting, and a full-size .38 revolver is the best compromise I could find between getting the job done and being easy to use for someone unaccustomed to firing firearms, recoil, etc.
If I were preparing to repel an invader who was after me or my family personally, I'd look at heavier guns, but there would still be the over-penetration issue, and I would still prefer revolvers, due to their immunity to feed jams. I would probably keep the .38 and add a short ("barely legal" for manueverability) shotgun with a wide range of loads on-hand. Actually, I plan to do that.
I do the same (keeping a broad range of loads in speedloaders in the safe) with the .38, so I can weigh factors like weather (thickness of clothing) and whether I'm alone in the house.