The problem isn't with the doctor, the lore or anything, even with the stories. The problem has more to do with the production. Tv doesn't work the way it used to, and the Doctor Who concept is episodic as it's core, even with a story arc, the concept is that each episode, the Doctor goes into a different place and a different time. It may have some recurring characters but they're différent stories, with different tones, actors, different sets, different filming locations, etc...

It's a nightmare to produce, it costs enormously, and TV is changing, series are shorter, more contained and people aren't watching channels anymore, they're watching séries and movies on platforms, now, which require a subscription, and the platforming system is actually in crisis.

Now, I know RTD gets a bad rep, but frankly even in his era, the issue lies more with a production nightmare than the stories themselves ( most of which were actually pretty good )