I broadly do the same, but with changes to phase 3.
I'd cut the Met back to a rebuilt Rickmansworth with longer platforms (and split the service between there and Watford), and convert the fast lines north of Harrow to OHLE for exclusive use of NR, before extending to Aylesbury to meet the phase 1 electrification. You'd need to add a new pair of tracks from the Watford triangle to the new Ricky station, but that's not too onerous. You could cheap out and skip the Ricky rebuilt and extra tracks by using Moor Park as the interchange, but I do feel reaching Ricky would be worthwhile, especially as it'll likely need a wholesale rebuild to lengthen the platforms for longer NR trains anyway.
You can then lengthen the platforms between there and Aylesbury to run longer Chiltern services to increase capacity. You would probably want to build some more southerly Chiltern/Met interchange platforms somewhere along the line as well, perhaps at Wembley Park, or ideally if you could make the room, West Hampstead.
The alternative is to extend the Met to Aylesbury and 4th rail electrify it, but you're going to get better journey times with NR trains - NR is likely more willing to upgrade the fast lines to a proper speed rather than the suboptimal speeds TfL maintains them to for the s-stock, which is optimised for acceleration and not top speed. They peaked at 62mph with the A-stock, but they should be able to easily handle 90mph+ for NR trains given the alignments.