It's probable that most of your incoming links point to the index page, so it will take priority for searches where it has relevant content.
You could go out and get links to the deeper pages, and optimise the content more effectively relative to the main page.
But it's probably much better to go with the flow, and just ensure that your visitors have good site navigation to take them quickly and easily where they want to go.
In practice, few people will be concerned at not being at the perfect page so long as the site is relevant - and they can move with just one click.
And it isn't a perfect science; change too much and you might get people at the deeper pages, who wanted the index page. And that's more of a problem, because you are probably more likely to lose people that way.
And they don't call it an index page for nothing ;)