Mapping app to plot several points
There's quite a few applications for iOS that support GPX track information, which you could probably use to sort of meet your needs. I won't list them all, as there's quite a few (free and paid), with various focuses on walking/riding/hiking or photography (for geotagging images).

I've used GeoTagr (formerly GeoLogTag) for quite a while for generating GPX files for geotagging photos. I believe you can copy GPX files in/out of it also, via iTunes (actually various methods to get the files out), but there are quite likely apps that make that process easier (try the ones designed for walking trails if you want easier import).

Again, there's many more, with many different features, so just do a search for GPX on the iTunes App Store and see what suits your needs (and let us know if any in particular suited your needs!).

Something like Trails Lite GPS Tracker or EasyTrails GPS Lite might be more appropriate as they're designed to import GPX track files also, to let you follow the trail. I see no iOS6 Apple Maps flyover screenshots, but that's pretty new so I'm not sure if it'll just come natively since they use the native iOS Maps API, or if they'd need to be modified to support such things.

Maps+ is another interesting one, which supports trails and bookmarking points (you'd probably need the paid version though). This one specifically uses the Google Maps data, apparently even with iOS 6. This includes elevation maps, which may be useful for tracks.

The caveat is most of these types of apps require you to use GPX files, which may or may not be a downside for you, depending on the current format of your data points. It's a reasonably common format though, and I'm pretty sure things like Google Earth can produce GPX files.

There's really quite a lot to choose from though, many with free "light" versions to test out...