Tom, the Cipro metro station is unaffected. You could use that one for one of your visits; it's not far from the Vatican museum entrance. Lepanto, which is abt. 7 blocks east of Ottaviano, is another option. Prati, the nice neighborhood it's located in (we stayed not far from Lepanto once) is safe and more residential than some other parts of the city.
We've also stayed just 2 blocks or so south of the Aberdeen and didn't think it was a bad location. Sure, it was a bit of a walk to some attractions but it was close enough to some others, and Rome is such an interesting city to walk anyway! Catch the B-line metro at Termini to get down to the Colosseum area, if desired. I would agree that the Piazza Navona area would put you closer to the Vatican, though.
I'm pleased that you want to take a stroll on Ponte Sant'Angelo at night. We made a point of crossing it at least once a day when we stayed in Prati: a favorite in Rome! There is a nice evening/night view of St Peter's dome from Ponte Umberto i? You might cross that one going one way and Ponte, Sant'Angelo going the other. A shot taken from that one:; Ponte Sant'Angelo is the bridge in the foreground. I've taken a shot or two of my own from that bridge.
https://www.flickr.com/photos/jon_w1/16429928087/