I haven't read all of the posts but, for the time being, doing something similar to what Abraxis states is pretty spot on for making a challenging game where you don't accumulate too much money. If you make the game challenging, you won't have too much money... Unless you sell research around, which I also consider an exploit (since they are priced far too high now).
Basically, there are a few problems with the economy, as I've seen it:
1) A big problem is there's nothing, save for military, that really costs you anything. Industry and research cost next to nothing. It's too easy to get your research up to full speed right at the beginning. The maintenance on Manufacturing Plants and Research, specifically, need to be higher. This would make it so that your industry maintenance costs are high and a part of the game. Currently, they are so insignificant that they can be ignored.
If you're paying, say, 1K in maintenance for each research plant that generates 20 research points, then that starts adding up. Do something similar with Manufacturing Plants and your industry also starts getting expensive.
In this way, industry and research also starts costing money to maintain. It will also make the research and manufacturing techs more worthwhile as you could save a lot of money if you increase your manufacturing and research plant's effectiveness.
2) Ships, Stations, and Space Ports are too cheap. I'm talking initial cost, not maintenance cost. The maintenance cost should not be 1/6 of the initial cost. The initial cost needs to be about 2.5x higher than it is now.
3) Disputed stations, techs, and the cost of wars all need to be greatly reduced in diplomacy. They are worth far too much as is.
4) And that gets me to another big part of the problem... the AI saves a ton of money. Which is why a lot of you also save a ton of money. If the AI spent more on military, players would have to do the same in order to keep up.
Unfortunately, these things aren't moddable. I really hope in the future these are either changed or made moddable, as I'd really like to change the ways these above things work; it would create a different economic model for the game.
Until then, just create a challenge, as Abraxis stated.