1) For the most part, I think the mechanics of the current system are sound. The problem is simply in the prices. Right now, during a boom, the price of metal/crystal is never going to go above the 550-575 range. At any given point during a game, your credit production is most likely to be 5-10x that of your resource production so at the absolute worst price, 550 for a stack of 100 is a fair trade. At any other time, 300-350 for a stack of 100 is a steal. On the flip side, it's almost pointless right now to go the other route and amass resources for transfer to credits because the sell price is roughly 1/3 of the above figures. Selling 100 crystal for 100-200 credits is almost always a waste unless you have an absolutely 'massive' stockpile that you know you're not going to use (which is highly unlikely if you're trying to keep up with a competent opponent).

And since credits are capable of buying at these prices at any time, you're always going to get better returns from a trade port than you will from a refinery so there's very little thought involved in choosing logistical structures.

2) As noted above, booms only boost the prices to a point that could easily be considered a fair trade. Unless you're really strapped for credits, you don't even have to avoid the boom. As for crashes, I don't see those very often as, given the current rates, resource sales happen very rarely if at all.

3) The prices have been adjusted in a way that gives resources more value so, yeah. I think it'll certainly help.

4) Right now, I think they're practically useless unless you have nothing else to research. You're far more likely to get a good return from research or development that improves credit income.

5) When you buy a couple stacks of something, the price goes up steadily. When you hit a boom, it doesn't happen instantly but the price shoots up very quickly to the 550 range. Generally, you'll be able to get all you need before the boom prices kick in.

Until 1.04 hits, no. Not really. A trade port will almost always be the more lucrative way to go.