This whole "problem" is not really unique to football but pops up in other places (eg, residential real estate markets where the seller typically pays their agent a fixed percentage of the sale price, although this is currently being disrupted a bit by new players like Purple Bricks; you also see this in banking/investing in the form of various fees but it is also being disrupted there as well).
It can be hard to properly calculate the "value" that intermediaries add, and they often have effective monopolies as well, which means bubble-like situations can develop where intermediaries are sucking an amount out of a particular economy that is disproportionate to what they actually contribute. If this is the case, usually somebody comes along with a disruptive solution that puts the intermediaries out of a job and lowers overall prices.
To be honest, I'm a bit surprised something like this hasn't arisen organically (e.g., multinational consulting firms offering flat-rate contract negotiating services to players), but in part it may be due to the fact that agents are more than simply brokers but also promoters, and that many players probably feel they owe their agent something for getting them to where they're at. Combine that with the low age (and therefore relative financial inexperience) of professional athletes and I guess it's not so surprising why things haven't already changed.
