@Rachnera
My opinion's in this post was formed after reading everyone's valid opinions on this thread, to try and add onto what's been said with my thoughts. At the end is a link to a game that did this, but with few villains.
If you're going to do a puppet villain and then a second main villain, the second being behind the puppet villain, then I'd recommend still introducing this main villain and change the plot to focus on them sometime during the second half of the game. Maybe a little sooner/later, but do it before getting to the end. Since, even if you met that villain before, or seen them a lot of times as another major character during the game, you won't have much time to do a sudden build up to that villain goals and motives and ture character if you leave it too late.
Same with a single puppet villain. Now they can be seen as the villain at the end of the game, if there actions until then are all revealed and truly exist as making them fit the puppet villain. Since we see there actions, there character can automatically build from there. But it has to be done well to be pulled of successfully.
Doing this successfully though, that would be good. I wish you luck, since I can't think of a true long-extended example right now from any of the many video games I use to play when I was younger.
Edit: Hang on, in a way I'd say Clouded Hearts has an example. It's a very liner example however, because there are only about 4 villains in total. I'd say both last two villians are puppet villians. Technically you could say there was an extra 5th villain for a while, but I don't count her. Yet story-wise she does fit as being controlled by the puppet villain and the real puppet villain too.
Link:
https://rpgmaker.net/games/6055/
It's an RPG Maker game if the link wasn't obvious, but done quite well. I played it a looong time ago. You can also find a more recent but still a few years old LP of it on youtube. I do recommend the game to anyone, but it should be of use for a good example of two puppet villains too.