The Ba'al haTurim explains that the world "VaYikra" is written with a little aleph because Moshe Rabeinu in his humility wanted to leave out that letter and write "VaYikar," as if Hashem just appeared to him by chance. Hashem overruled him, so to speak, and the letter remains, but Moshe's modesty is acknowledged by its being a small letter.
Last post we discussed R' Akiva's ability to squeeze derashos and halachos out of every dot in Torah sheb'ksav. Even the crowns on top of the letters contain deep meaning. If so, imagine the wealth of Torah that might have been lost had an entire letter -- the letter aleph -- been omitted from the Torah! How could Moshe have thought to leave it out?
R' Shach (Rosh Amanah) answers that Moshe Rabeinu weighed that wealth of Torah against the lesson in humility that could be learned from his leaving out the letter and Moshe must have concluded that the lesson of humility is the more important one.