I use the WSM as-is, no modifications, with one exception: occasionally I substitute a 2-gallon Brinkman charcoal pan for the stock WSM waterpan—a step made unnecessary in the 2009 models, which have a larger waterpan.
If Weber asked me to re-engineer the WSM, the only permanent modification I might do is weld the access door flush and shut. Though Weber improved the access door in the 2009 WSM, it is still somewhat flimsy. As many here know, if the door is not latched properly, it can fall open, resulting in excess air, an overheated cooker and severely singed BBQ. I know many people use this door to refill the waterpan, but poking a rubber hose through the access door over glowing-hot charcoal to refill the water pan always strikes me as dangerous and dumb.