Every version of D&D has a genie in a bottle hidden within the pages of it's "rules". That genie is in the finer details of the rules themselves; and what those details do to the game and what they imply for it's play. Rule expansion, like genies can provide enormous boons, and bestow tremendous tragedy. As made clear in the beginning of the Castle Keepers Guide from Castles & Crusades,
"Tyranny of the Rules
The Castle Keepers Guide is a book that presents the C&C player with a host of new rules and options for their games. In some respects it simply builds upon existing structures, making them more useful and playable, while offering no real impact upon the way a CK [GM] runs a game or what is allowed. These options simply expand the game. In other cases the impact these rules carry can be staggering. ... they can change the nature of the game you want to run. Take caution while expanding your game with new rules and options. The more rules that you add to your game, the more clarity it gains, but the more freedom of action you lose." (CKG p. 7 bold emphasis mine)
And before you believe that this is a unique phenomena to C&C consider what the Pathfinder Core Rule Book says at the opening of it's book,
"The Most Important Rule
The rules in this book are here to help you breathe life into your characters and the world they explore. While they are designed to make your game easy and exciting, you might find that some of them do not suit the style of play that your gaming group enjoys. Remember that these rules are yours. You can change them to fit your needs." PF CRB p. 9
All games, yes even First Edition Advanced Dungeons & Dragons made it clear that the final arbiter was the GameMaster, and the players. Though admittedly some systems make the optional component less optional than others, GMs have and will continue to ignore, forget or simply exclude certain rules from play; as well as add personal embellishments in the form of "house rules".
The problem, or potential problem is that, as Stephen Chenault Says above, adopting certain rules or playing with the full spectrum of the rules releases that genie from the bottle. Some players may love and revel in the ensuing chaos. However it is undeniable that the nature of gameplay will change with those additional rules.
What really makes a D&D game distinct is its own unique genie in a bottle. Take for instance D&D 4e. For the first time the game could not be played without minis and battlemaps. And each class acted based on powers. Those rule changes unleashed a genie. And in the case of 4e a very powerful but well controlled one. However, that essentially warped the game--and I use word warped intentionally here. Warped in the sense that everything became skewed, unusual and different; in the same way a real warp makes space and time seemed changed from before. The experience was different. The core was the same--classes, levels, hp, initiative, d20, saves etc. But the experience was different. Some felt it was good some didn't. It was still D&D, but a different genie had assumed control.
And lest some mistakenly assume that the change is always additional rules, consider 0e or Labyrinth Lord, or Swords & Wizardry. They release a genie in the form of less rules. The genie there is a free wheeling anything goes sort of genie, where all player expectations and GM creativity has had the walls torn down. Very truthfully, such games accept only the barest bones of what D&D is and let you, as Gary said "Imagine the hell out of it!"
Many people assume the genie is the game instead of the core. But that's not true. Because I've played all versions (except 0e), and many of the clones, and truthfully I play them almost all the same. I don't open any genies I'm not comfortable with. On the other hand I always open the alignment genie (a particularly volatile and unpredictable one at times.) So, sure there's a rule or two we use here and there specific to a particular edition or version, but it's still essentially the same game. Which in a way makes me realize how wonderful a thing Gary and his canting crew came up with those many years ago: a system so robust and strong, an idea so powerful, a movement so fundamental to the imagination that time, the market, culture or age could not dim or diminish in any way*. And that my friends brings me a great deal of peace.
* Now it's time to make my caveats clear. First and foremost I am very aware that Gary himself expressed great displeasure with 3.5 in particular and the direction WoTC had taken the game. I value and respect that. I have used his quotes to that effect often in my own debates in various edition wars. But I would cite for Gary his own reasoning in RolePlaying Mastery where he makes clear that some elements in the game can't change without changing the basic nature of the game. An act that he himself had done when he changed the game from D&D to AD&D. I'm not begrudging him this; just pointing out that lack of consistent thought is the bugbear of great minds. And the opinion of the moment is oft influenced by outside forces more greatly than we might admit. Minds and thoughts develop, as did Gary's. His evolution as game designer took him away from D&D and was already doing so as he contemplated the second edition of the game. Sadly we never got to see that. So, in my mind I pay homage to Gary even while disagreeing with some of his opinions, by stating that the core elements of D&D may be even more basic than he himself admitted in RPM. --