It was a throwback. FFIII had a out-of-nowhere boss that wanted to return everything to nothing after you beat who you thought was the final boss. Zeromus also came out of nowhere. FFI you didn't know what the final boss was going to be until you got there.

When I first beat the game, having only beaten VII, I thought it was pretty weird, but 10 other FF endings later, it was a good way to end it for me.