Lillie was a surprisingly minor character in the manga. The manga was 33 chapters long and she only played a major role in five or six of them. Sun and Moon were the co-protagonists, with Gladion being the next most important. Sun and Moon were also given completely different backstories - Moon was a girl genius from a prestigious family in Sinnoh who was an expert on poison and pharmacology and specialized in poison-type pokemon, while Sun was born in Kanto but his grandfather was from Alola and had his land seized by the Aether foundation to make the Aether Paradise.
There wasn't a lot of ship-teasing in the manga, either. The closest it got was when Lillie said she really, really looked up to Moon. I was disappointed with the ending - it felt incredibly rushed. They set up all these plot points and just couldn't resolve them all by the time they finished with the manga.