It's kind of reasonable to deprioritise the Bakerloo, even as someone who used to use the Bakerloo very frequently. Bakerloo gets significantly less usage than other lines: Piccadilly has double the number of annual travellers than the Bakerloo, for instance.

(It'll be interesting to see if Piccadilly usage numbers go down now Crossrail has been finished and some portion of Heathrow travellers switch over.)

The Bakerloo itself is also kind of a weird, redundant line. The NW segment doubles up with the Watford DC line, and for a lot of NW destinations like Wembley, the Jubilee and Metropolitan are better choices.

There was also the issue of the proposed extension out to New Cross and/or Lewisham. They probably wanted to put off making a decision on the rolling stock upgrade until after they'd decided whether they were doing the SE extension.

Bakerloo line trains are about the same age of the Picadilly line, but the Bakerloo line is less used, so presumably that has edged the Picadilly ahead. They are next in line, as the article notes.

The Central line are on much more modern stock - the 1992 stock, and are currently undergoing a renovation programme, so the need to replace them is less pressing.

coming soon

All three lines, and Waterloo & City, are planned for upgrade.

They’re working through a process of rebuilding Central line trains, updating virtually everything it seems.