If you're looking for retro games to be anything more than pure fun, you're looking for the wrong thing.
Retro games are popular for that specific reason: They are fun, and nothing more.
Try playing Contra, its general regarded as one of the best NES games, yet you won't find anything thing deeper than, "Hey lets kill some stuff."
These days, people (developers especially) seem to thing that making games fun is a little bit beneath them. Its like they are trying to convince themselves that at the end of the day, all they are really doing is playing with a toy. Yes, the 360 is a toy, so is the PS3. You're lying to yourself if you think otherwise. A definition of the word toy is: Something that is specifically designed for fun.
I for one am sick of modern games that try to be some work of serious fiction. The result, more often than not, reeks of pretention.