I would first of all change Peter's design if possible, cause I just don't like this one but it doesn't bothers me enough. Second, I would have left Rhino for later seasons and worked in Mysterio. I would have given Eddie more emotional ties with Peter, concerning their past, rather than borrowing heavily from Ultimate. Another thing, if this doesn't happens in upcoming episodes, get Venom to beat the crap out of Black-Cat just like in the comics, I just don't like her.
Story-wise, I would try and adapt some events from recent comics than starting from the beginning in every incarnation. I would maybe perhaps devote a whole season to events pertaining to Civil War, I really liked it because it made sense that government is finally doing something about masked vigilantes, forcing them to register if they want to continue being heroes. Because to me personally, I don't know about others, I feel that this "Yay you saved us regardless of the damages to the City and possible loss of life," just doesn't works for me 'every time', comic or not, it just doesn't.