I would be happy to see the economy reworked step by step: commodity by commodity. It takes A LOT of time, yes, but if you are determined enough it will be doable.
I would start with the resources like ore metals, basic goods (food?, water?, oxygen?), consumer goods, &c. ... and then move onto the parts/products (for example Optronics), followed by the final products (Computerthingies). Work out what base uses what to produce what and go by that regarding buy and sell prices. The "credits/second"-profit can be balanced independently, if you set a buy location, outgoing from there all sellprices (for those bases that accept the freight) go up depending on (minimal) flight time and (maximal) risk.
Planets need to buy and sell more than normal stations - unless they are specialized (and sparsely populated / one-commodity-production "only") planets like Juno or Kurile. (Stuttgart has a rather high population, I'd guess they got more than just food production, but mostly food production. If at all they got some non-industrial production as well, but heh. Just an example of "smaller difficulties".)
Trade depots of course buy and sell. If the cr/sec is set right, it could be made in a way that you can both buy and sell one and the same freight and make a good profit in cr/sec in both directions for it.
Once you have an automatization for the cr/sec setting, setting the sell/buy options shouldn't be a problem!? No idea what you got in that regard though.
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The problem currently is, that many bases don't have much connections. It might seem like they do, but actually you always get send in (small) circles after some time. I felt like it was better in the old setup. What bugs me most though, are a few things:
1st: some bases have a CRAP ton of metals, of which almost all go to the same place for actually varying prices - no point in taking x when y makes more profit.
2nd: planets mostly only selling alcohol (with decent cr/sec profit).
3rd: the things mentioned in part one of the post; bases NOT BUYING things they need (for a good cr/sec price) and NOT SELLING things they produce or SELLING things they don't produce iRP!
4th: lack of locations to buy basic goods like mining machinery at in houses; some goods should pretty much be in-house trades or SHORT RANGE TRADES - one house + its bordering indies (Basic Alloys, Mining Machinery, Consumer Goods &c.), while other goods should be LONG RANGE TRADES - inter-house trades, from one house to another house or further (Quantum Multiplexors, Optronics, Gate/Trade Lane Parts, (rare/special) metals, (Ship Hull Panels?), &c.).