Haha I know the feeling Hasuak. Been thinking about the same thing on and off for over a year now and have only come to the conclusion that it's probably best to try a minimalistic approach to both the gameplay and the story. Not only will that make it more doable in terms of scope, but I think the two will be able to play along more nicely if theyre not fighting for dominance.
Like Arima suggested, it may be wise to rework the story to see if it can fit with different kinds of gameplay better. Maybe have the story told in a subtle way throughout the game, where the player would have to fill in a lot of the blanks. Have you ever played Out of this World? It's a pretty good examples of this.
I personally also feel that combat heavy gameplay kind of distracts me from story... I think adventure type games are better for immersing players but the challenge there is to make it feel like you're doing something even when you're stuck, else it can get boring fast. Most people these days don't seem to have much patience for obscure, often nonsensical puzzles and such.