As far as the economy is concerned, I would say BB is structurally very similar to Hattrick (which is probably a feature). I've been around Hattrick since 2003, so I've had the chance to follow the economic phenomena there a bit. As an economist (I'm a Ph.D. candidate at Clark Uni in Worcester, MA), hopefully I can provide an insight or two that can be useful.
To boot, I completely agree with your assessment about game calibration. A thing to have in mind is that BB is somewhere in its late infancy, as far as game maturity is concerned -- both in terms of number of seasons and number of users. I would expect at least 10 or 15 seasons before things start clearing up a bit.
My take is that trading should be regulated naturally (taxes on transfers, team chemistry drop), not artificially. This means one should probably avoid stuff like direct wealth tax and limitation of the number of transfers, which will be, by definition, arbitrary. Put structural limits in the transfer system and let the market play it out.
An implication of having multiple trained skills is the fact that any sort of transfer compare will be hugely ineffective. For one, there will be a huge price volatility for the same level of primary skill(s) based on secondaries. Consequently, market scanners are almost guaranteed not to work due to the lack of enough comparable transfers. For those who play HT, the situation will be comparable to the TC for wingers -- they compare 5 skills, and there are barely ever enough matches for a meaningful comparison. And HT is significantly bigger in terms of transactions.
Likewise, I am also skeptical about an automatic bidder and its ability to assess prices correctly. Not to mention that it will needlessly complicate the market.
I think 3) is almost a necessity at some point, and one might also play with the magnitude of the transaction tax to reach a good trade-off between financial gain and team chemistry penalty. However, it should be structured in a way, in which one shouldn't be able to offset the enthusiasm drop with the ability to purchase and maintain the wages of significantly better players.
What has to be considered for the long run, though, that once teams 'saturate' with players to the level where all their income goes for wages, the economy will be hit by a sharp liquidity crisis. As in, the more saturated teams there are, the less disposable cash there will be out there for transactions on the transfer list.
There isn't really an easy way around this structural flow. HT regulates by counting on having enough 'unsaturated' teams and a good amount of new teams, which inject fresh liquidity on the market. However, this approach is only of limited use, as multiple ticket price increases were needed over time in order to maintain a healthy amount of cash fluctuating around.
Maybe one of the solutions will be to introduce a luxury tax type of feature in the end of season. I haven't thought about this much (and it will likely have to work exactly the opposite way that real NBA luxury tax works), but I guess I can post again when have I spend some time rationalizing this idea in game terms.
"I don't know half of you half as well as I should like; and I like less than half of you half as well as you deserve."