Well I'm not an SM expert, but I am prety sure that Setsuna's powers
aren't terribly potent in manipulative terms. I mean depending on the
version, stopping time will either kill her or banish her from reality for a
time.
Still, there are a lot of possibilities that can be explored about time,
paradox and other fun topics.
Let's see.
I recall once reading a short spamfict where Setsuna's power over
time came from the true Key and Guardian of the Gate, Yog Sothoth, and her
true mission was to manapulate the Senshi so that they eliminated all
potential opposition to the Old Ones besides themselves.
There's a lot of possibilities. She could periodically work with time
guardians from different universes, perhapse a WOD refference where she's
sometimes self conscious about being so incapable at the things
Wrinkle-Sensei tries to teach her about time.
As far as a villanous Setsuna goes, the key to handling is to get a firm
idea of 1: her goals, 2:what she's willing to do to accomplish her goals,
and 3: what she's capable of actually doing.
For instance, if Setsuna could make precision time jumps and keep her
past selves very aware of what would happen, she would be capable of some
very precise manipulation of reality, and would actually not have to push
for that much sacrifice and strained convictions. If on the other hand, she
can only send other people on imprecise trips to general periods of time,
she has a lot less manipulative capability, and might require more
ruthlessness.
And of corse the chosen goal is vital. You could do one where she's
obsessed by the need to impose order on the world, and is working to try and
purge most of the random elements of human nature. You could do the Old
Ones angle, and have her setting up the world so that it will only have a
small handfull of beings with any capability for resistance, then taking
them out with surprise. You could do a story where the timeline changes,
and she's so obsessed with preserving what she knew that she actually tries
to start the calamity's leading to the creation of Crystal Tokyo herself.
Or you could have it secretly turn out everything she's ever done was to
manipulate the timeline so a guy in the 30th centure falls for her.