.....in the early days, Ki training was the primary focus and I believe Tohie's methods will get you that foot in the door. His four principles of Mind and Body coordination are a good place to start to establish your internal skills foundation - but it is not the end, only the beginning.
.....For those looking to get started, there is still plenty of material out there available on Tohie's stuff - but once you get an idea of what you need to do, you absolutely must get with someone with these skills to get the proper feedback for making adjustments in your training - it just cannot be done any other way.
I think one of the many problems stems from the (conscious or unconscious) burden most if not all of the uchi deshi under O Sensei would have carried, from feeling they were the representatives of him and his Aikido, along with the effect that had on their egos. O Sensei approached and formulated things from a particular place, in a particular fashion, with a particular set of experiences, inclinations, and gifts that were all unique to him, and when he passed, I think most uchi deshi had to find their way forward by themselves, or in groups of like minds.
It's fairly well-known that O Sensei didn't answer many important questions for them, including a lot of "how to" processes, on both the practical and spiritual levels. Those who took up the task of providing those answers have formulated, and teach, what they believe to be correct. Because, in my opinion, most if not all (Tohei, for me, initially being somewhat of an exception) didn't have the complete picture, a lot of what they have passed down in Aikido became a practice of only a partial aspect of the art, often missing the key (or Ki) ingredients that made, and make, Aikido…. Aikido, and distinguish it from being simply a system of jujitsu based on "aiki-type movements." They came up with their own answers, but have been lacking because they weren't ultimately sourced in the same things that O Sensei's Aikido was, and for me this is a real problem. I'm not talking about Shinto per se, more the training and experiences he had that made him conscious of the deeper skills that come from subtle physical, energetic, and spiritual training.
There are various ways one might describe these "Aiki skills" - centering, energy dispersion and release, ki musubi and tracking at the energetic level, ki power, kuzushi (and tsukuri) at a whole different level, Kinesthetic Invisibility (my original teacher's term), even spiritual guidance - these, and more, in my experience, can be taught and learned.
Some people have more of an affinity (or even a gift) for this stuff than others; that's natural, and that can express itself in various ways, depending on inclination, intention, and need. If the basic training is sound, virtually everyone can get it - that is, experience it, learn to access it, and do/apply it. It's how much or deeply they get it, and where and how far they go with it that is the distinguishing thing.