I don't see why that is a problem. It's not as if the same character could do all those things, you still had to choose. So far as I can see it makes no difference if you make that choice at "choose a class" or "choose a subclass" level. Mechanically, the outcome is the same, and it cuts down on repetition. You only have to explain psi points once rather than copy-paste it into several classes.
In 5e, subclasses have a certain amount of mechanical heft to them. This heft is limited.
When they melded them together in the Mystic, you ended up with combinatorial explosion of abilities. You got a chassis that (in theory) supported a full featured melee character and a ranged spellcaster controller. What more, you could basically be both if you wanted.
And then there is the core class features. They must be suitable for all 3 flavors (tanky, skirmishy and castery) as written; if you split it, the core class features also split.
You'll notice that I hijacked one of the subclasses for Soul Knife and Immortal, then layered a subclass on top of each. That gives a lot more design room to build a skirmisher or tank, and we don't have to either (a) put a full "kit" into one discipline, or (b) make disciplines useless unless you combine the right set of them. Both of those problems are in evidence in the Mystic.
Combinatorial explosion is also a big problem as written. Notice above, I took a bunch of abilities which (alone) are at least somewhat reasonable, stacked them on top of each other, and got someone who can do the damage budget of 3 top-level spells in one action.
So we end up with it being challenging to construct a character, challenging for designers to know if the class is completely broken OP or not, unclear what kind of archetype the subclasses actually represent, subclasses and classes that are mechanical bundles of abilities more than coherent story seeds.
As a concrete example, the complex mastery concentration mechanic looks great for a psion who is some kind of cerebral meta-psionic character. For a soul-sucking psionic vampire, a psionic body-melding perfectionist, empath who emotionally boosts their team, it is looks sort of strange.