I’d break them down like this:
MINES, FORESTS, HERB GARDENS AND MANA SITES produce a ton of one single resource. If you use this resource - or if you have reason to believe it’s super disproportionately valuable and want to play a dealer in one specific resource - then go this way.
FARMS AND BUSINESSES give you just over a Throne in cash. This is actually a fair whack - especially if you like buying drinks and gewgaws with your IC cash rather than things that make your stats go up, this is the choice for you.
FLEETS start to get to the point where you’re plot-influenced. You need to think about where you send your fleet, because the world cares - only a little, you’re like 0.5% of the Empire’s total shipping capacity - but the winds of international diplomacy blow on your sails. Or you can support the Imperial navy, which is occasionally really really useful!
MILITARY UNITS care deeply about the plot. You ~can~ just turn them loose to gather stuff for you, but you can also get pretty good returns by paying attention to the military game - also, right, you’re contributing directly to the war effort, to the tune of 2% of the power of an Imperial army all to yourself.
CONGREGATIONS are for plot. A Congregation gives you effectively a loudhailer to talk to the smallfolk of the Empire, provided you can get your Assembly to agree with you - you get to be probably around 10-20% of your national and virtue assembly, unless you’re Highborn, then it’s more like 5%. People need your vote and will come looking for you, and you’ve got the chance to put in a Judgement, which can do things like have people executed or excommunicated, take advantage of a plot mandate or sway the hearts and minds of the people. The price you pay is that a Congregation’s income is paid in liao, and liao isn’t very materially valuable - although it is the only way to power the use of priest skills.
There are magical enchantments that boost everything but mana sites, effectively selling mana crystals for a return in whatever your resource creates. All of them are within the reach of a coven of five or so - some of them can be cast by a lone magician, if they’re a good one.