I believe adjusting the values for trade ports, as well as potentially changing the way they work (so as to make trade ships much more valuable a target), alongside reducing the cost of creating a refinery / making refineries more efficient.
If the sole purpose was to nerf trade, then adjusting the return values for trade ports would be the easiest and most direct way to tackle the issue...another complementary change would be to reduce the bonus determined by the length of your longest trade route (currently set at 7.5% per node)...
These changes are easy to implement and would almost certainly be effective in reducing the power of trade...and if that was your only concern, then I agree that messing with logistics would be kind of silly...
So, refineries become more competitive, but only because trade ports are nerfed...I personally would rather see refineries buffed to the level of trade ports, and I most favor a simple cost reduction (which may be all that is needed)...
Changing logistics is not the most direct way to nerf trade...more to the point, those proposed changes really are more targeted at exacerbating diminishing returns (something that is more controversial and probably an entirely different discussion)...changing logistics in that proposed manner reduces the impact of trade relative to your other economic assets, but it doesn't really nerf trade per se...after all, each trade port costs the same and yields the same returns...
I guess it really becomes a discussion of semantics...changing the logistics mechanism would not nerf trade on a per port basis, but economies invariably would depend less on trade (and refineries) and more on tax income and extractors...whether that actually qualifies as a nerf to trade I'm not so sure now, and I probably should have been more careful with my wording earlier...
Here is a series of changes I have worked with that seem to reduce the power and importance of trade:
1) Use the new logistic system suggested above
2) Change the trade length bonus from 7.5% per node to 2.5% per node
3) All ice/volcanic planets now spawn with 3 or 4 extractors instead of 2,3, or 4...
4) Base extraction rate is raised from .46 to .5 (it is important to note that currently the actual base rate is .4, but on normal speed the economic modifier is actually +15%, which raises it to .46...I'm working with a base of .5, but with an economic modifier on normal speed of +0%, so for all intents and purposes extractors go from .46 to .5)
5) Reduce the cost of refineries (the exact credit/metal/crystal has yet to be determined, but let's just assume it is exactly equal to that of a trade port for now)
Change 1 is more for diminishing returns, and equally affects both trade ports and refineries...change 2 is a direct nerf to trade ports (which consequently makes refineries more competitive)...change 3 is mostly to prevent those awful bad luck ice/volcanics with only 2 roids, but it does slightly raise the average number of extractors any given refinery could pull from...change 4 makes extractors more important relative to trade, but it doesn't actually help refineries become more powerful (two different values in the entity files)...change 5 makes both structures have the same capital costs...
In general, changes 1, 3, and 4 make trade and refineries less important relative to extractor income (ie trade and refineries makes up a smaller percentage of your economic output)...change 3 however means that trade is nerfed more than refineries (if only very slightly)...change 2 is a direct nerf to trade ports, and change 5 is a direct buff to refineries...
You could toy around with the actual outputs of trade ports and refineries as well, but so far I haven't done that...