I have enjoyed exploring bunkai in a systematic (and I hope reasonably comprehensive) way for a long time now... I have alluded to this in Facebook discussion groups, but I don't think I have ever discussed in detail the "formula" or "system" I use to do this. So, I think this may well be the first time I have shared it publicly.
I ask you to keep this in mind, as this is very much a rough first draft of my thoughts on the topic. Each of these "levels" could occupy many pages worth of exposition to do them justice. However, outside the context of building a body of knowledge with a student over the course of years, I don't think that additional level of detail will really be very meaningful.
I have only systematically analysed the 3 Naihanchi kata using this formula... I suspect this can be done with most kata, but I don't want to give the false impression that I have done this with all the kata I know.
These are the "levels" (used informally and very broadly) that I use to systematically explore the applications of a kata's movements:
1) Understanding applications of individual techniques as standalone waza.
2a) Most of those waza can be done inside or outside.
2b) The same standalone waza at an increased level of detail (ie vital-points as targets etc).
3) Understanding that each kata movement has a relationship to the movement after it, in that the subsequent movement can be used to address an opponent's attempts to defend themselves (from your prior technique)
4) It therefore stands to reason that all movements (except the first) also have a relationship to the movement preceding it. In other words this level explores chains of techniques that are three movements long. This is highly pragmatic because you control one of the opponent's hands on the first movement, you control their other hand on the second, guaranteeing the third technique should be unimpeded.
5) It therefore necessarily follows that long chains of movements can be strung together (often the length of the entire kata), with the opponent attempting to defend against each technique, with you using the next kata movement to counter their defense. This illustrates how the kata is highly proactive in forcing an attacker's moments.
6) Most of these long chains can be worked on the outside and on the inside.
7) The same principle should also work on renewed offense or semi-continuous offense... as opposed to just countering an opponent's passive defensive movements (ie the opponent's blocks).
8) It is necessarily the case that each kata movement is only followed by a single movement in the kata. However, it would be enormously foolish to believe the kata designers gave you *only that single option* for a follow-up technique or a counter to an opponents defense and/or renewed offense. Kata is far more cohesive than that. The movements in kata like Naihanchi were carefully selected so that they work not only with the subsequent motions but *also* many other motions throughout the kata. At this level those alternate combinations are explored.
9) The next level of bunkai studies is to examine whether each of these "alternate combinations" (or alternate follow-ups) work on both the outside and inside, and whether they work against both a passive defense (blocks) and against renewed offense (this won't always be the case, but it usually is).
10) Naihanchi (and most likely other kata) is quite intentionally designed to contain counters to all of its own technique (gyaku-waza). At first this is done as standalone gyaku waza (counters to bunkai levels 1 and 2 above).
11) It stands to reason that if the kata has gyaku-waza to all its individual techniques it must also be possible to construct gyaku-waza for combinations of those same techniques (still only using the waza explicitly shown in the kata). These should be worked against all the levels 3-9
12) At this point, the kata should be comprehended a cohesive fighting style which is able to address a multitude of possibilities and eventualities. It is no longer a collection of waza. Nor is it merely a collection combinations. It is not even just a system of proactive control. It is a rational, systematic, and reasonably comprehensive fighting system (in, and of, itself).
13) Through the use of kakie and resistive free-fighting one should be able to express these all those levels spontaneously and in response to ever changing circumstances but still staying entirely within the kata (only using waza presented in the kata). This is going from understanding that the kata is a self-contained fighting system, to being functionally able to use it as a fighting system.
14) The next level is the extension of principles and technique within the kata beyond what is explicitly shown in the kata (ie implicit options within the kata). For instance, the kata shows one elbow strike. This level asks "what other ways can we use an elbow strikes, and what other types of elbow strikes can we use?". The kata shows a particular wrist-lock against a specific grab. This level asks "when else can we use that wrist-lock and against what other attacks?" Techincally other terms especially "henka" might be better designations for this level of application principles. Other terms might also possibly be used such as oyo, findi, ura-bunkai and so on...
15) Exploring "extended principles" (or implicit techniques) in a way similar to the explicitly illustrated waza in the kata (ie levels 1-13)
I think this could potentially take a decade or more worth of study to fully explore.