While they do share a very similar animation style story-wise and thematically they are quite different.
First Flight focuses the story on Hal and, as the name might imply, is a retelling of his origin as well as his introduction to Oa, the Guardians, and the GL corps. It is also a linear tale, beginning with the origin/introduction then developing into more of an intergalactic crime thriller that wraps up in a summer blockbuster/sci-fi type of climactic encounter.
Emerald Knights, on the other hand, is in more of an anthology-type of format. Meaning it presents a number of short stories, in this case various shorts about different members of the GL corps you may or may not know and/or care about, within the context of a larger story where Hal is relegated to more of a storyteller role than protagonist.
And though the animation and character models are almost identical between the two movies they establish temselves as two entirely different continuities.
**** Mild to moderate spoilers **** While Hal is a novice in First Flight and Sinestro becomes his evil arch-nemesis during his initial training; in Emerald Knights Hal is the mentor for a younger lantern and refers to Sinestro as one of the lanterns he trusts the most. ********
I found both movies quite enjoyable, but I am a big fan of both Hal Jordan as well as many of the individual corps members. YMMV