7 Wonders Duel is great, and even better than the very good original.

Patchwork is a very good space-filling tiling game. Its theme and premise may sound boring, but it is fun and very competitive.

The small city-based Ticket to Ride variants play two players very well, and are also good with 3 or 4 players.

Tak is a great abstract strategy game for two players.

Concordia is an excellent game, and plays very well with two players on small maps (e.g. Cyprus or Egypt).