The Neo Geo Pocket Color has a fantastic card battler called SNK vs. Capcom Card Fighters Clash that comes in SNK and Capcom varieties. Great game on a great system. Pairs well with the unbelievably good fighting game on the same system.

pokemon tcg 1+2 (English patch) for gbc is super fun

There was a Magic: The Gathering computer game in 1997.

Arcomage was released on Windows in 1999

https://www.mobygames.com/game/2815/arcomage/

There was also a recent DOS miniature version for a game jam, which I cannot find again.

What do you define as a retro system?

Pokemon TCG 1+2 are all that come to mind, for me. If you want to stretch the definition a bit, the Megaman Battle Network series for the GBA has a deckbuilding aspect to it, but it's more of an action RPG.