By your third museum, everything starts to look the same. Statues have the same stance. Paintings have the same subjects. And it gets harder and harder to differentiate which piece of art you saw where. And yes, I realize that might be offensive to some art history majors/art buffs out there. But art is just not my thing.
But despite all this, I still wouldn’t have skipped the Borghese. A trip just to see the villa and the grounds would have been worth it. It’s also located in (around?) this park so you can explore that too while you’re at it.
In order to get into the Borghese, you MUST make reservations. If you don’t have one, don’t even bother showing up. That’s how exclusive this club is. The museum is open from 9 am to 5 pm and tickets are available in two hour time slots. You can use your Roma pass on the Borghese as one of your comped sites. I’m not sure how much the reduced price with the Roma pass would be but a full price ticket is 11 Euros (as of September 2014). But again, you just have to reserve ahead of time, and let them know that you’ll have the pass. Then when you arrive, just show them the pass (that you will have bought) and voila! You have your ticket in! Their site also says that every first Sunday of the month, admission is free (with a reservation) so if you happen to be in Rome then, it’s an awesome deal!