Mako showed a lot of character growth in episode 7 and it was payed off in episode 12, I really do think that the Mako-Ryuko bond has been one of the high points of the series.
I like Mako's relationship with Ryuuko, but (even after all the family-related stuff in 7), I feel like I have a much stronger sense of Mako's investment in the relationship than vice versa. I know why Ryuuko values the familiarity of the Manshoku household, but I wish I had a better sense of how Mako's presence stabilizes her mood.
It feels weird to say this given how much information was usually packed into any given episode, but it still feels like a lot of characters wound up underdeveloped. I think it would have made a big difference if the Elite Four were more strongly defined with their own philosophies and views. Everyone exists in such thrall to Satsuki, and Ryuuko's opposition to her is so simplistic and petty, that it's hard to get texture for them and for our protagonist. Uzu and Gamagoori feel more human than the other two, but their development takes more time because Ryuuko's confrontations with them are just power versus power, arranged more or less arbitrarily.
A strong second half could make these points less meaningful, but I feel like the show squandered some of its potential, especially in the middle stages.