what version you playing on?
your trade port usage is most likely incorrect. you want to make the the farthest route possible between your two furthest trade ports. that means it may even be a benifit to not have trade ports on certain planets to force your trade chain to be longer. and you can and should build more. no reason at all to stop at one per well. on the planets with trade bonuses, you should be building 5 or more, once you get the +logistics research.
and... the mid and higher tier mining boosts are genarally not worth the money... expecially when your only on 6 wells.
thats economics...
as far as battles... did your enemy have subverters or overseers? those support cruisers are fantastic, and you need to take those out first....
as well, you should have a decent quantity of support cruisers your self, the command frigs are not that hot, but you need lots of hohos. i am sure you had 3-4 repair bays as well? repair bays + hohos = 60 hp healed per second. not easy to crack.
you should post a replay of your game so we can see what you are/were up against.
Id love to post a replay showing you how to expand... give me a sec.
file uploaded: http://www.mediafire.com/?8vnpa51a6ai6nnq
you will want to place this here: C:\Users\<username>l\AppData\Local\Ironclad Games\Sins of a Solar Empire\Record-MultiPlayer
and then you can watch it under an option in the single player menue.
as you can see, i skipped over 2 volcanics to colonize a ice near my oppoenet.... it didnt work out so well, but as you can see, i initially skipped over the tougher planets, and colonized them in later, and sent colony frigs to other astriods out in the system. dont forget the neutrals, they are important to grab as well.