This phased approach is very peculiar to me. My parents are currently in the process of refitting their kitchen and reorganizing the layout of the ground floor of their house. The Arriva Rail Northern approach would have seen them replace the units first, and then set about knocking walls down around them!
To be fair their are only a limited amount of places capable of doing all this work, and a huge amount of demand up and down the country. So this may be limiting what work can be done when. Plus your parent's kitchen isn't needed to transports hundreds of people around the place, there could be operational reasons that they can't afford to keep some units out long enough to do everything, like other units breaking down. Phased works like this is not an uncommon thing, indeed right now it's happening in my office! Works are planned in seemingly odd ways, but often it comes down to the availability of contractors and the logistics of keeping a minimal level of service running. Let's not forget that Northern's fleet is run very hard, and they don't have much wriggle room right now. I would imagine that accessability mods are far more important that charging someone's phone.
And anyway, most people travelling on Northern services probably won't get near enough to USB sockets to even use them until a lot more capacity is released....