My main complaint is that your decision of what to build (marketplace vs. library) is not based on what you need (revenue or research).
As noted, I agree that this dosen't work well in Civ4.
Here's another way that Civ5 might help improve this though.
We can still get a good differentiation between research vs gold buildings IF they can give us incentives to move things in the right direction.
The real problem occurs because currently, if you build a gold building, that lets you shift your slider *away* from gold towards research.
Whereas what we want is for buildnig a research buidling to increase your tendency to shift the sliders towards beakers, but building a gold booster to increase your tendency to shift the slider towards gold.
What we need is more things you can do with gold.
The real problem comes fromt the fact that about the only thing you can do with gold *is* to convert it into research.
If gold were something valuable in its own right, then by building banks everywhere, you'd want to switch your slider more towards gold, since for each point of commerce you put towards gold you now got 50% more yield than you used to, whereas your yield from each commerce put towards science was unchanged.
We know you can buy terrain with gold. So that's something. But maybe there need to be more things you can buy. Bad news if unit upgrading happens automatically/free now, since that's about the main use for gold we have.
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Another way to fix the problem is to move sliders to the city level rather than the empire level. There is mild evidence for this from the screenshots where we can't see any sliders on the empire main screen.
The problem with this would be that it encourages *too* much city specialization. Basically every city will be set on either 100% beakers or 100% gold, and will only bother building one type of booster (gold or research).