I'm not really sure about advice I could give you, seeing how I haven't actually played The After Years myself. But I can tell you that the first 2/3rds of the bosses are old FF4 bosses that follow the general pattern of their original FF4 counterparts. Also, Ultima Weapon, Deathgaze, Omega, and Shinryu are all optional for the last 1/3.

As for teams, the original team (Cecil, Kain, Rosa, Edge, Rydia) and "Cecil's family" team (Cecil, Golbez, Ceodore, Kain, Rosa) are the most used teams for the Final Dungeon, from what I've seen on youtube.