Max out planets and use trade ports especially in a string. You can see the string by hovering cursor over credit total at upper right of screen, it will appear white over the phase lanes. The longer the string the better income you get from trade ports. Have to experiment with what planet to have trade port no know formula explains how string is figured. Any planets that are in the white string line max out trade ports. If playing Entrenchment use starbases with trade port expansion. Make sure to research other available technology like cargo holds, if playing Advent there is nothing for cargo holds the TEC has 4 and can make credit hand over fist. Hope this helps.

If playing TEC, try building Trade Ports on most of your worlds,

If playing Advent, do the same as TEC but with broadcast centers (they increase the alligeance % level, giving you more tax income),

For Vasari, matter processors are the answer (you can have more credits by selling your metal/crystal).

Loyalty doesn't affect trade port income.  It does affect refinery income, however. 

Typically the trade port is a better investment than a refinery, especially far away from your empire's core where loyalty is low.  However, extractors in neutral space are unaffected by loyalty, so if you're next to a couple of asteroid belts with plenty of extractors a refinery can be a good idea.  Try to make as long of a trade port chain as possible, as this increases the income of all your trade ports.

Yes be mindful of how you build up your fleet. Every fleet upgrade takes up x% of your income going from 9 in first upgrade to 75 which can really slow you down. I usually dont go this high unless I have a serious amount of resources laying around and every thing else is researched.