While I am sure AGA could and should have done a lot of things, I assume it comes down to money.. and TfL is spending rather a lot on doing things its way. Meanwhile, the GA franchise didn't include spending money on stations (especially once it was known that TfL was taking over some services).
Now, I know that a lot of people moan about what they get for the money they pay on their season tickets, but I assume that TfL has to get its money from somewhere too? I am sure someone will point out that TfL has actually cut some fares, but my point still stands - someone is paying for all of these improvements.
Don't get me wrong, I do like the LO way of doing things. Clean stations, staff from start to finish of service etc - but it isn't free. It reminds me a bit of when Homer Simpson was put in charge of sanitation and spent his whole budget in a matter of days - but, boy, did people have a great rubbish collection service for that time!