As far as academics are concerned, SPA Bhopal is better in my opinion. This is backed by the fact that SPA Bhopal requires higher JEE Paper 2 ranks for admission into its B.Arch program. Additionally, SPAs are dedicated to Architecture and Planning studies. So they have a higher branch value in the field of Architecture.
Now, MANIT Bhopal is also a good college. One advantage is that it is located in Bhopal city. On the other hand, SPA Bhopal is located on the city outskirts.
For branch value, join SPA Bhopal. But for a better exposure to city life and the associated advantages, join MANIT Bhopal.
Even though I’m a B.Arch student at MANIT Bhopal, I will offer an unbiased opinion on both these colleges-
I would recommend SPA Bhopal over MANIT Bhopal. However, first try to reach out to some seniors from SPA Bhopal to get a clearer idea of the ground reality over there.