This might sound crazy : if assimilation is thisway because of performance that get pretty bad in late game, would it be possible to have an option to switch between the one we have now and a "perfect" assimilation that work great but create performance problem ?
Probably not a switch in game, but there are mods that do just that IIRC - check out the user-made mod forum. Or alternatively you can play around with the values for assimilation yourself by adjusting various levels in the files common/pop_types.txt and the poptypes folder, until you find a balance that works best for both your gamplay preferences AND your own individual computer's performance running the game.
In the end though, given how much a large segment of the player community on here complains that the game already runs too slow (to the point of almost not running) in late game even with the current ahistorically high assimilation rates, it would be very unexpected at this point for Paradox to reduce assimilation rates UNLESS the resulting reduction in assimilation speed is accompanied by other changes to ensure that gamespeed is not further compromised in lategame than what it already happens to be.