In the Ramban's introduction to Sefer Bamidbar, he describes the Mishkan and the encampment as a replacement/portable version of Har Sinai. Har Sinai has fulfilled it's role and Bnei Yisrael have moved on - the message, not the mountain, is the key.
Shem MiShmuel describes the desert as the antithesis of life and Bnei Yisrael's sojourn in the desert as a war against this force of evil. Before any war a census needs to be taken. A census gives the population a feeling of self-worth.
Why weren't the flags given until a year after Matan Torah?
Rav Soloveitchik on why Ephraim and Menashe aren't always listed in the same order.
Delivered at the OU Israel Center, May 30, 2019 (25 Iyyar 5779)