Felix, as secondary antagonist in one game and protagonist of its sequel, is in a rather odd position for this question. In the first game Isaac fits two and three, and during that time Isaac probably thinks of Felix as his nemesis. Then, for a while, there is no nemesisness, although Felix is decidedly unfond of Karst. Then, post-canon, he's got it in for [SPOILER]Alex[/SPOILER].
Frederic is, frankly, not effective enough to have a nemesis.
Going back to a long-ago former pup for a moment, Picard has no greater opponent than the Borg.
And for potential pups... Kain has a slightly odd situation, given the allegiance changes over the course of the game. Golbez, Cecil, Zemus... any or all of the above... And, if you believe (what I've heard of) the sequel, his own dark side.
Doroga doesn't really have any nemeses. There are people he dislikes - Atsurak, for instance - but he's not built for carrying a grudge.
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Frederic is, frankly, not effective enough to have a nemesis.
Going back to a long-ago former pup for a moment, Picard has no greater opponent than the Borg.
And for potential pups... Kain has a slightly odd situation, given the allegiance changes over the course of the game. Golbez, Cecil, Zemus... any or all of the above... And, if you believe (what I've heard of) the sequel, his own dark side.
Doroga doesn't really have any nemeses. There are people he dislikes - Atsurak, for instance - but he's not built for carrying a grudge.