Monopoly is the first game that pops into my mind. It gets so boring yet the layout is really good. I think even a minor change would make it much better and that change would be stacking. If the game allowed stacking, I think it would be alot more interesting.
Judge Dredd, while not a bad game, could be so much better with better rules. It has a fantastic layout and is fun to play as is, but it would be so much better if the layout was better utilized.
Johnny Mnemonic, again not really a bad game, would be so much more with balanced rules. I own one and really enjoy it, but the spinner is the thing to light and hit. Nothing else comes close. The modes are fun, but not worth enough points. Back in the day, I was hoping the guys that did the Matrix would release it as a kit. I love the layout of JM -- it's brutally fast -- and the Matrix looked fun.