For me, the main negative point is the linear progression of all the tech lines. If you want more manufacturing, there is a single line of techs that will give you better factories, and no other line of techs will help you. The same goes for research, wealth, tourism, etc. Thus, pursuing a given goal requires no strategic choice or evaluation of trade-offs - there is only one option (ideally, the tech specializations would give at least some choice, but as is discussed elsewhere, there is generally one clearly superior option).
I actually made a proposal regarding a more interesting tech tree back in December 2013 - you can still find it here.
