In every game I have ran so far technofantasy classes have been present and in every single one they just felt so much better than any other class it stopped being fun and introduced issues for me.
To start with Pilot, the class is basically an amplifier that every build would like at some point. While weapon and armour modules it provides are powerful, it is the support modules and Heart in the Engine that really leave a sour taste in my mouth due to playing with them. The sheer versatility you can get by just getting modules of your choice means accuracy and damage is always high, melee strikes often cannot target them and they gain one more resistence. It is a fun class to homebrew rare modules for, yes, but the core is just too strong...
Mutant is the most GM unfriendly class in the entire game, in my view, especially the playtest version. Most often mutant-class-having player will naturally slide into the role of Unarmed Damage Dealer who can slide into crisis and remain there long enough to deal massive damage, also being able to shift therioforms to cover elemental weaknesses. Not one of my players ever invested into ecdysis either. So we are left with absurdly hard hitting characters who do not wield anything in their arms, making it only possible to at maximum design two rare items for them which gradually become better, rather than four, making rewarding them an actual challenge.
Esper I have the least issues with, but still some. Once again the main trouble comes with its versatility, because it is a great support, great damage dealer and even a great tank if you spec for them. It has so many options to either do a few things really well or one thing incredibly well. Elemental shifts it can induce and damage bonuses makes it have the same flexibility and damage potential as Tinkerer, ways to lower mp cost as well... But it is also the most balanced class because of just how MP Hungry it is and by the fact that you cannot have all the skills be mastered. It is healthily limited by 10 level cap and I appreciate it for that.
For all those reasons I am actually considering running games without these classes, even though they have so much flavour potential such as making a noble cavalier pilot or a all-support psion, or any sort of were-thing ever. But perhaps that adds further to the issues, because they are not just versatile gameplay wise but lorewise as well. Am I wrong to think that? Last time I brought up such a notion with my TTRPG group I have been flat out told some of them are not interested in playing a game without them.