You're looking for a simple answer to a complicated question. You probably won't find what you're looking for.
The best method to learning is the method that works best for an individual. Things like Anki, teaching others, qbanks, textbooks etc. are just tools. As a generalization (important), the best methods to learning are going to involve "active" learning - something that forces you to recall, integrate, and re-organize the information. QBanks are the best at this, IMO. People will most likely see the best results when employing a combination of techniques. Anki is good for memorization and recall. Teaching others is a good way to test understanding. QBanks are a good way to test integration and application.
As for Anki being superficial, it's kind of true, but that's not a bad thing. Anki fills it's niche. If you want to have a concept down, there are parts that kind of have to be memorized. Take pneumonia for example. There's lots of superficial details that need to be memorized - what type of pneumonia do certain organisms cause? What are the presentations of typical and atypical pneumonia? What are the drugs of choice? This is all high-yield info, and Anki is good for getting that stuff down.
Other stuff lends itself well to teaching others as a way to solidify your understanding. What is the pathophysiology of pneumonia? Why does it present the way it does? What's the immune response? Why are certain physical exam findings relevant? Reasoning through this stuff is a good way to make sure that's all straight.
QBanks and other methods are a good way to test the integration of the above.
This is obviously very superficial and not a one-size-fits all - there's lots of resources and techniques I didn't even touch on.