I'm not sure I follow, run what?
So... character development systems with the following combination of attributes wind up...
bad.
A - There are permanent methods to boost your stats, but they are either limited in number, or with an ever-increasing price, where the increase in price is significant and matters. Effectively, one way or the other, you have limited "upgrade slots", by either soft cap or hard cap. This game has the "increasing cost" version of this in a number of categories.
B - There are ways to extract additional long-term benefit from each slot that require more up-front effort, but better long-term payoff. This game has this, in using different varieties of qi.
C - Once you've spent an upgrade slot, it's locked in permanently. If you spent it in a less efficient way, then you have permanently locked yourself out of the benefits that someone who did it a more efficient way would have gained.
D - The highest tier of "more up front cost for more long-term benefit" either doesn't exist (you could always push further) are is expensive enough that it is not practical to put off using the slots entirely long enough to start with it.
/*******************/
If you have A, B, and D, but not C, then the players can put in the effort to get the upgrades at a lower tier, and then replace them later. This is fine. It winds up being a bit of an interesting optimization dance of which levels to use and when to convert and whatnot, but as long as the additional overhead from tiering up your upgrades is manageable, it's not a problem. Actually, "interesting optimization dance" can be kind fo fun, for certain sections of the playerbase.
If you have A, B, and C, but not D, then the players can put off actually using the subsystem at all until they've gotten powerful enough in other ways. In this case, that would mean never physically cultivating at all until we'd gotten The Best Qi to do physical cultivation with... and then doing the same with meridians, and doing the same with breakthroughs, and... you get the idea. Having to put one or more of the subsystems on ice for a potentially extended period of time isn't necessarily
great, but it's still manageable.
If you have A, B, C,
and D, then you are basically telling your player base that there
is a Good and Right answer, and they aren't allowed to use it, and must instead do this other thing that is obviously worse, and that their character will be inescapably weaker forever as a result. Right now, this game is almost purely an econ game. "Numbers go up"
is the point. For a game like this, forcing the player base to make choices that they know are bad, and thereby diminish themselves forever feels
really bad. Even if you're just pretending, and you later retcon it to not-C, it
still feels Real Bad.
So please, please do not do this thing.
Does that make it make more sense?