No I meant antagonist. Before SRTT came out I always had this thought that the Boss would become the main antagonist of SR3, with the Saints becoming a titanic foe that a new character would have to take down.
This is sort of a tricky thing to pull off.
Mostly because games tend to make you feel awesome, or the main character is better than the rest.
As a result, having the main character from the prequel as main enemy means they have to be toned down alot in order to be beaten, or has to rely on (often) scripted circumstances.
Examplary in this case would be Prototype 1 and 2, Mercer and Heller respectively.
In 2 you have to face against the main man from 1.
First off, Heller did not feel nearly as powerful as Mercer did, so the fact that you could actually defeat Mercer felt...unlikely.
To top it off, Mercer was so very much toned down that all who played the first game felt this was a joke, because Mercer had MANY abilities Heller did not have to begin with (full bone armor etc) and several attacks (devastators).
The one Heller did have, seemed much much weaker too, but Mercer did not have any of these as the enemy.
To make matters worse, some of the abilities Heller did have were also locked out and it was simply a pitiful grudgematch with the enemy using a scripted attack plan with just a lot more health than you do.
It was confined to a small space, with lots of scripted events.
As third option, which is also risky, is that the new main character is simply even more powerful than the last, but that runs the risk of making everything else in the game feel underpowered.
But generally speaking, I'd strongly advise against using the player character of previous games as an enemy in the next, unless it was a highly realistic setting to begin with and the player character never had access to skills/abilities any other character couldn't have either, so not being superhuman in any way.