In Era 3 it's now possible to buy all ship classes from Mesophon. My personal impression is that you would be insane to build ships yourself given how cheaply Mesophon sells some of them, especially because ship costs are based on a deprecated metric (the era 2 ship power values, which are otherwise not even in the game anymore!)
Selling resources to Mesophon: How much is an AE worth?
When you sell resources to Mesophon (either through a T&E trade route or with transports), Mesophon pays you AEs. In theory for all resources 1 ae = 20 WUs. AEs are not subject to attrition, unlike ships and most resources, so you always get maximum value out of them. In practice, AEs can be obtained much more cheaply; I will use Hexacarbide, Light Jumpdrives and Organic Food as three example trade goods, explaining my reasoning below:
Mesophon pays 0.5 aes/ton for Hexacarbide. Hexacarbide has a supply-chain-adjusted WU cost (SCI WU cost is sensitive to the trillum cost of refining hexacarbide) of 5 WUs per ton at "abundant" frequency and 10WUs per ton at "major" frequency (assuming that the trillum supply is of the same magnitude as the hexacarbide supply) Abundant deposits of both trillum and hexacarbide are common throughout the galaxy, so we can easily assume that all of our traded Hex comes from abundant deposits.
Trading hexacarbide, getting 1 ae costs 10 WUs
Mesophon pays 0.002 ae / ton for Organic Food (only T&E can trade this efficiently, since you would need millions of jumptransports to move it around). Organic food has no supply chain and very low WU cost , 0.04 WU/ton; on Earthlike worlds this is reduced to 0.02 WU/ton; on Ocean worlds it's ~0.2286 and on Desert Worlds it's 0.032 WU/ton. Let's assume all our food is coming from Ocean worlds, which are common throughout the galaxy. (My New Agraria empire last year was structured around organic food sale.)
Trading organic food, getting 1 ae costs 11.43 WUs
Mesophon pays 4 aes/unit for light jumpdrives. Light jumpdrives are made from trillum but are primarily a value-added product, with ~90-95% of their value coming from the WUs used to build them. This means a trading empire with poor planets can build light jumpdrives anywhere and resource deposits will form only a minor element of their ae value. Lets assume all our jumpdrives are using trillum mined at "major" abundance, which means they cost 80 WUs per unit.
Trading light jumpdrives, getting 1 ae costs 20 WUs
Clearly, a trading empire wants to exclusively sell raw materials extracted from abundant deposits, although selling organic food is also viable if there are more earthlike and ocean worlds than are needed to supply the extactor worlds. Worlds without abundant deposits should serve as hubs, foundations, infantry academies and citadels. Selling ship components is a sucker's game. Now what about buying?
Buying ships from Mesophon: What will an AE get you?
Mesophon ship sale prices are based on the OLD (era 2) ship power values. The ratio of AE cost to ship power was AEcost = era2power x 1.2, rounded to 2 significant digits.
This results in some incredible bargains on low-tech ships! Look at some of these examples:
Anywhere "WU equivalent AE value" exceeds the rate you getting for selling minerals, you can buy that ship class from Mesophon more cheaply than you could build it directly! This is because a major element of ship cost is their direct unit WU cost; their resource WU cost can be reduced by using abundant minerals, but the direct WU cost is never directly discounted by any game mechanic. In a Mesophon purchase, you get to use 100% discounted WUs if that is what you are selling to Mesophon. For an empire selling "abundant" minerals at 10 WU/ae, pretty much any low-tech ship is available instantly from Mesophon at or below its direct-build cost using the same abundant resources!
Since AEs do not undergo any attrition, if you sell resources for a week and then buy a ton of ships, you are also getting the equivalent of a full week of production all at once without the normal losses from attrition during the 1-week period, which I believe can be 30-40% depending on ship class (some calculus is involved).
Change Mesophon's ship costs to reflect supply-chain inclusive WU cost. I recommend using the equation (AE_Cost = SCI_WU_major_abundancy_cost/8) * ((minTL+2))/10). This makes all ships slightly more expensive to buy than build even getting the best possible deal, but trading empires will still get the benefits of no attrition, instant fleets, obscurity (nobody knows how many aes you have) and not having to muck around with complex supply chains, not being dependent on chronimium abundance to get high-tech ships, getting capships in distant locations without having to ship them across the galaxy, etc. Adding a minTL modifier for ship classes makes high-tech ships slightly more expensive than their low-tech equivalents, which I think is a decent compromise since they normally require more complex economies to build.
It might also be worth considering a very small "tax" (attrition) on AEs as well.
Here are SCI WU costs, for reference: