N vs Ghetsis was a simple Pokemon battle between one of the Old Legends under N's Control and the Third Legend Kyurem. That still isn't any where NEAR being similar. N wasn't even said to be the leader of the Old Team Plasma, he's basically a more helpful Red in the new games. Only reason we associate him with Plasma because he was with Plasma. Also Ghetsis WANTED to absorb the Dragon N was carrying so they didn't stop a conflict between two legend. N lost the battle against Ghetsis and had his dragon stolen. The fight wasn't resolved by a Third Legend, but incited by the third.
The events on B2W2 are not similar to the events of R/S/E. There is still only 1 Evil team in B2W2 not 2 evil teams.
Obviously Emerald and B2/W2 final events seem not similar if we look at details, but looking at simplified scheme they seem to be similar:
1) Two conflicted leaders (or ex-leader in N's case) are responsible of causing fight between two legendaries by awakening them or bringing them to one place,
2) Two legendaries fight,
3) Appearance or creation of another legendary/another form ends the fight,
4) Player is not capable of catching any of seen legendary Pokemon during the final events. Emerald and B2/W2 are the only games with that trait.
I mean that if there is similarity in story scheme in Emerald and B2/W2, it could mean R/S remakes with Emerald story addition in gen 5. Because G/S/C and D/P/Pt also have similarities in story scheme, such as going by boat to new land after beating League or receiving Togepi egg during storyline (in Platinum).