So who’s gonna win between the two gunblade users? Both are swift and deadly. Lightning is fearless and skilled fighter, with high agility. Meanwhile, Seifer undoubtly has high endurance and stamina (HP), this character might hold reputation as loser (mostly because the game needs one to make Squall a legend), but sometimes surprising with his creativity.
Lightning is a stable fighter, bold and cool, therefore her focus is undoubtly better than fragile, insecure and unstable Seifer. With her high agility she will have no dificulity to dodge Seifer’s attacks and read his moves, then shower him with deadly strikes combine with magic attacks. 
Mean while talented but mental damaged knight Seifer will have to learned Lightning’s fightning style and moves first before jumping into the battle to give her unpleasant surprise in fight (ask Odin for this). The fact that he could slice Odin in one blow, shown how much strength he has, and how sharp his gunblade is (actually took great sense of timing too). That scene also proves that Seifer could move faster than Odin, but by statistic, he shows nothing special in agility, means that Seifer can move fast, but not all the time.
Seifer always focused on himself, how he could be more powerful, how he can crush his enemies with his own various deadly attacks, rather than watching the enemies in the middle of actions and judging their strength (which is why he always lost to Squall). Meaning, altough he is a creative fighter, but the creativity is seems not spontaneus. Adaptable Lightning will see this flaws and win her momentum by retaliating Seifer’s attacks easlily.
conclusion :
Lightning undoubtly will dominate the fight, unless if Seifer could control his mental stability, then he could probably be more worthy opponent against her. But, there’s till chance. If Seifer wants to beat Lightning, he must do it quick, as quick as how he kill Odin. Because in long term battle, Lightning undoubtly will win the fight.