Very intelligent thread. I´ll give my own 2 cents about it.
Designing your ships to be cheap can make out a great difference - something not to underestimate esp. in the earlier stages of the game. Using Yor in TA as an example here, there's a big gap in the beginning-weapons cost: the Missile gives a ATT+2 - but costs 50mp, while the Mass-Driver costs only 8mp, giving ATT+1. It is much better now to use the cheaper Mass-Driver as your weapon, because the ships can be built 3 or 4 times faster as the costly one. Your ships will only have 1/2 the ATT - but you'll have 4 times of them, giving you 2 times the ATT-rating and 4 times the HP. So, if you wanna find out the efficiency of your ships design (in terms of Military Might ranking) you'll need to take the cost-factor also into account.
A further advantage of the "cheap ship design" is that your ships have a lower maint (which might be outweight by the fact that, over time, you'll have plenty more of them, though). Plus, an upgrade is more cheap, thus, it's still doable only to built empty hulls (who are maint free) and upgrade them to warcrafts once the need arises.
About the "free" survey-module: Don't built that wonder - built Eyes of the Universe instead. It gives much greater sensor-range without having to equipp anything.
I always go for miniaturization instead of huge hulls, and instead of big weapons I´ll use on type defenses. This is much more cheap, you're able to overrun the enemy during the beginning/mid parts of the game. And avoid being soked in by Tech inflation (esp. in TA) on weapons (which you can get/trade from the AI's)
Keep your fleets always busy at war against weaker opponents (even if you don't plan to invade their worlds) so they can destroy a lot of ships and gain some levels, and these "strong ships" I´d later upgrade to a fast and expensive best-weapon/defense ship that can intercept enemies alone.
I´ve made the experience that tiny hulls added to a fleet are almost always attacked first - and thus get destroyed. Thus, adding them prevents damage from the rest of the fleet who get an upgrade on a constant basis.
About the transport modul, well it depends. If your plan is to invade a planet with only 500 troops of course the normal modul stuck on a tiny hull is most cheap. But I wouldn't do it - because what do you want with a planet that has just a few people on it, it'll drag your economy down and the pop grow rate is really low. Better to leave some people there to get it over 2.500b people ASAP, and for that you'll need the big transports. The only reason for the "cheap low-yield transports" I see is if are going to attack a big planet by using Mass-Driver on it, decimating the population until you are able to take the planet normally.
