Do the enemies in One Piece get better in future arcs? Not really feeling the vast majority of the CP9 guys.
One Piece's villains are at their best when there's one charismatic leader at the helm. CP9 doesn't really have that and sort of splits roles up among a few characters, like having Spandam serve as the actual boss when Rob Lucci is obviously the big bad in terms of muscle but has no real personality. The arc is amazing despite the absence of a truly great main antagonist.
I love the main villain of the next major arc after Enies Lobby, but he's also just as likely to annoy the shit out of people (which is part of why I love him).
One Piece's best villains are real magnificent bastards. Guys like Arlong, Crocodile, Doflamingo, etc.