There are a number of issues with the manual driving (on the Jubilee and Northern - the Central and Victoria are both completely different) -
(1) no one has really explained the finer points of the system to drivers, and that includes instructors. Some have picked things up by making their own observations or getting snippets of info off people in the know, but there’s been very little formal instruction. Straight away this leads to a confidence issue, or people making errors because they don’t understand why the system is behaving in a particular way in a given location.
(2) to achieve ATO comparable run times the train has to be driven on the limit of what is allowable. This means always driving within a second or two of the system intervening. Many drivers aren’t comfortable with that.
(3) Driving close to the limit will cause lots of over speed imminent warning alarms to sound in the cab, which some drivers find irritating. Regulars zone out of them and don’t even notice, but this isn’t everyone’s cup of tea.
(4) The driving style is different because the train is very much more powerful than before, so motor/coast/motor/coast driving is unavoidable if one is to keep rigidly to the speed profile. Many drivers find this uncomfortable or annoying, or find it too much of a change from what they did before. Likewise some drivers are simply not comfortable hitting a platform at high speed and relying on most or all of the service braking capability available to stop on a sixpence (especially on the Jubilee with the platform edge doors which require a tighter degree of accuracy).
(5) the system retains a *lot* of software glitches, and learning where these are and how to work around them requires a degree of dedication - bearing in mind what I wrote above that one is always within a second or two of the system potentially intervening.
(6) I’d also add that successful manual driving also requires a good awareness of gradients. Most drivers won’t have this. One doesn’t fully appreciate tunnel gradients unless one has actually walked the whole line!
All of the above is a lot of hassle compared to pressing two buttons and sitting in peace letting the train do the work!