Barriers to Green Building
Luckily most of the barriers to green building are just limitations put on by the client, builder or architect, but building codes, zoning laws and cc&r's, and availability of materials can also be barriers. In many cases there are work-arounds, but in others there aren't: if you are up against your set-back there is nothing that will allow you to stretch the building any further in the east-west direction. Even when there are work around, the added cost and psychological stress is a significant barrier to many.
Dealing with Barriers
The best course of action is always to start by asking questions and understanding why the limitation is there. Whether the barrier is imposed by a government agency or by neighbors, making them the enemy has not often been a successful strategy. In many cases, the way cutting edge green ideas were first accomplished was via a long conversation between the builder/designer/client and the code official. Code officials will often follow the lead of code officials in other jurisdictions, so that is one avenue. If the issue is one that can be stated in engineering terms, having a engineer design it and put their stamp on it is another path. Compromise is yet another path. This often leads to less than optimal designs, but such is the nature of being a pioneer.
Limitation of Material Supply
It is always best to know what materials are available and what they cost before designed. For example rather than just assuming you can buy an FSC lumber package, it is best to find out what sizes and quantities of those sizes are readily available and design using those as much as possible. Likewise with reclaimed materials or any other non-standard material.
Homeowners Associations, CC&Rs
The purpose of the additional restrictions placed on by CC&Rs are to enforce a level of uniformity, typically aimed at aesthetics and other similar things. In most cases they are benign, but can be a real thorn when it comes to putting PV panels on a home, or eliminating required turf grass. The biggest issue with these restrictions is that they are typically created with an aesthetic in mind that is very different from the ones associated with green building.
Green Building Codes
There are few things more frustrating than having to comply with some green building code when you've done all your homework and are trying to build a very deep green building. Alas, the codes were not written with you in mind, and if you're lucky there will be a simple prescriptive path that will keep the quantity of paperwork to a minimum.1 With the increased focus on green building there is no doubt that the number of regulations will undoubtedly increase and flaws in both regulations and green rating systems will end up being the topic of heated debate. The problem is that it is exceedingly difficult to regulate "good" behavior.
Notes
1: California Title-24 is an example of the worst case possible. You fill out a lot of paperwork, they tell you what kind of lights you can have, but they ignore how much PV you put on. In the process of trying to build a zero-energy/zero carbon house, I've found few easy work-arounds. You end up buying lighting, dimmers or occupancy switches you don't want and then changing them as soon as the inspector is gone.
I'm not opposed to reasonable regulations, but they shouldn't make doing green building any harder than it already is.