Huck, you (and the ex-Mayor) seem to be proposing a solution for which there is no problem. The only "blocked" project you point to is the Edgewater which, I hope you realize, went through in spite of the recommendations of the Landmark Commission. In the meantime, the developers had to address concerns that the then-Mayor and a certain alder wanted to ignore, and the whole issue of the use (and abuse) of TIF funding was brought out into the light.
Frankly, it looks to me like the process worked just fine. The council, in its generalist wisdom, voluntarily limited its ability to ignore the recommendations of the LC by requiring a 2/3 majority. After a LOT of public debate, the 2/3 majority voted in favor of the project. What is the problem here? You got what you wanted, didn't you?
As to the LC having a 2/3 majority requirement for over-ride, that makes absolute sense to me. If a project really is a wise move that is being irrationally obstructed by the LC, then there should be no problem finding a 2/3 majority of the council to over-ride. On the other hand, this is an area--unlike, I would argue, the Plan Commission--in which deference must be made to preservation and restoration over development. Once something is gone, it is not coming back, whereas redoing a strip mall incompetently just means it has to be done again. The LC provides a balance of interest against development wiping out historical buildings and neighborhoods, which could themselves serve as a resource in the future--but only if they haven't been torn down.
Furthermore, defenestrating the Landmark Commission would set a terrible example for other citizen committees that render decisions the elected officials disagree with. We have enough problems getting the city and the developers to pay attention to the neighborhood plans, for example. Yes, the pace of development is slowed down when we have to consider more than business interests. So fucking what? Why should they weigh more than the rest of us, especially when they're using our money to shape our city?