If you were to take out Darth Sidious in episode 1 and 2, you would need to either replace him with someone, or you would need to cut all the related scenes, which would reduce the quality of the movie.(quality is already very very low and many other scenes already need to be cut, you would lose some scenes you can easily salvage if you have a replacement character. If you opt not to replace him and decide to cut him out altogether, you will end up cutting all of the scenes that has Darth Maul in them as a consequence, since most of the time, and in some vital points of the story, they appear together. You would end up with a movie where a sith appears out of nowhere, kills a jedi than just dies. Because most of the backstory scenes has Sidious in them. And after Yoda says there is always two, it would take 2 more movies for the other to appear and it is at the very ending.) Now, you can’t replace him with any other character who is not sith and if you replace him with a new character, whatever character you replace him with has to appear in the other movies for continuity and will need to properly die since that character wont appear in the original trilogy. That would mean editing many scenes along with adding some new scenes, which would be a pain in the ass. (I am probably explaining what I have in mind really poorly, but I hope you understand what I mean)
Rather than try to edit Sidious out of the scenes or to replace him with another character if you simply blacked out the face under the hood and changed the voice then you could imply any character was the bad guy appearing with darth maul.
Imagine if that’s how it had been done and you were watching the movie for the first time (with no prior knowledge of the films) then seeing a character hidden in that way you would naturally try to work out who it was (out of the other characters that you have seen in the movie). Now if you added Dooku as part of the jedi council, then had him appear at Qui Gon’s funeral, and later add a shot of him finding Maul’s body, this would cast a lot of suspicion on his character.
Only then when we get to episode two would we have access to a scene where the Jedi discuss Dooku having left the jedi order, and Dooku explains he was Qui Gon’s master. If we then changed his lightsaber from anything other than red, green, or blue and avoided scenes with him and Sidious together, then across the two films this would add a lot of background to Dooku as well as make him seem like the main suspect for being Sidious so it would appear as if he had been a much bigger part of the movies, without having to try to edit him into all the scenes to directly replace Sidious under the hood.