I think the way they could have nicely balanced out using tadpoles vs not using tadpoles is by actually making them an interesting Purity Vs Corruption seesaw mechanic by taking the current brain system and have it act as a choice between the two.
For example here's a concept;
Choosing to remain pure or consume tadpoles would benefit the player based on this choice by providing miniscule passives or alternative Illithid abilities.
Where there is an actual passive offered however such as the Favorable Beginnings; the benefit would either defensively affect the player or offensively affect the enemy.
And the way the player would get to unlock them;
Illithid abilities could be unlocked at any point by consuming tadpoles, since they act as a powerful temptation in the story
In order to unlock Purity passives however; the player would have to progress the story up to a certain point without consuming any tadpoles. If they resist the temptation, then for example at the end of ACT 1 when speaking to the Guardian they'd be able to fortify parts of their brain against the tadpole's influence and become able to unlock the purity passives as a reward.
By using the Illithid Wisdom dialogue choices without consuming any tadpoles; the Purity bonuses would decrease by 10% for each use up to a maximum of a 50% if the player gains the True Soul tag, since this actually slightly reduces willpower which is reflected by the story in ACT 3 through Wisdom checks.
This way this whole system would not just be a "consume & forget munching simulator", but act as an emphasis of Corruption vs Willpower. And more importantly would not clash against the lore of the tadpoles enhancing us.