The internet has proven to be quite resilient. So there's not much to be changed. I can think of:

* More security baked in by default.

* Quicker implementation and standardization of features the market demands -- so Java, Flash and ActiveX could be avoided.

* Lesser reliance on central nodes (nameservers, etc), with a larger emphasis on a network of peers, which dynamically grows with actual need.

* Oh and somehow fix domain system. I don't think there's any value that domain squatters provide to the network that don't have simpler alternatives.