I noticed that throughout the whole Manga and Anime, there were many hints of the Allen X Lenalee pairing.

Examples in the Anime:
When Allen was apologizing to Lenalee for trying to sacrifice himself, Lenalee put her packet of dinner on his head, the music played was called Awakening of Love

Lenalee thought of Allen a lot when Allen was in China trying to get back his Innocence. Allen managed to hear her voice ( telepathy?)

Examples in the Manga:

Why would Lenalee wait for Allen outside the toilet if she was angry with him.

When Lenalee gets encased in the crystal, Allen was thinking of her.



Of Course, there were many more, plus, you should look more at the part where either of them blushes.