I agree that organisational structure is the single biggest challenge to agility. I see so many companies organised around legacy technology platforms that any project involves multiple teams each with their own backlog and priorities. Delays occur at every handover and are usually lengthy.
The problem with changing this is that so few organisations actually value speed to market. If how long it takes doesn’t matter (as long as it’s “on time”), there is no incentive to change the structure. Hence, agile transformation efforts only go so far.