I don't know if it's me or my playstyle but i didn't had much trouble trough the story even without ms.
My playstyle is simple, i just level up my starter only, and i didn't had problems with Sabrina, nor Morty.
For Giovanni, an easy tactic is to catch a sturdy magnemite and teach it thunder wave, this way you outspeed mewtwo and rek his ass.
For Kanto E4 it was a pain to grind a lot but at the end i felt satisfied by beating it, like in every handheld game the E4 is way too easy to be called "elite", in pro the E4 is a REAL elite. (i also got lucky with the rng xd)
For Claire it was a little difficult but getting access to Dragon Den solved the issue, i just leveled up my starter there and caught some poke lvl 50 and leveled them there since i was leveling only my starter in the story.
Johto E4 was easy since i already had my Kanto E4 team ready on the PC Storage ^^