I don't have any problems at all with the story missions not giving much money outside of the heists and some special stuff. I feel it fits with the theme of the story really, really well. Most of the story in GTA5 is about people dealing with their personal problems. When the missions are actually about getting rich, the payoff is big and that makes it more consistent with the risk the characters take for the money. Otherwise, the only times they risk their lives is when there's something they actually care about at stake - their own lives, their freedom, the lives of their friends and family, their passions, etc. It's a great narrative.
But what I do have a serious problem with, is the way properties are handled in the game. The stock market is fantastic. It works the way its supposed to, and there's a high risk when playing with the system outside of the scripted stock movements due to missions. On the other hand, the property management in the game is nonsense. It's poorly designed and balanced, and feels like the weakest link in the game's optional content.
The price you pay for most of the properties don't match up with the returns, and even worse, there's no way to influence the returns or get a refund. You can't sell properties back, you're stuck with them. You can't do optional stuff to improve the returns of the property, even though that makes sense and would have added depth to the game system. If you buy a cinema or a bar, why aren't there missions which you can do to improve the popularity of those businesses? Why can't you invest further into the business by paying for upgrades, marketing, or renovations?
Instead all you get are crappy ass missions from time to time which only serve to punish you if you don't do them by reducing your already low earnings. It's really awful. First you pay lots of money for something that doesn't get you much in the way of returns. Then you have to do garbage filler missions which add zero benefit to your returns. And if you fail those missions or don't want to do them, you end up making even LESS money that week.
Aside from the properties which do give you huge benefits like the Nuclear Waste Disposal Facility and Los Santos Customs, it's actually a bad idea to buy any of the properties in the game. You get no simulation enjoyment out of it, you lose money, and there isn't even good gameplay unlocked. Truly a terrible system which was rushed in at the last moment. Disappointing.
With regards to there being a lack of ways to make good money, I think I agree too. They should really have considered having more sports tournaments too, which are challenging but offer good rewards for those who want to take part in them. A golf tournament, a tennis tournament, doing daredevil stunts for a TV show, etc. The gameplay systems are already there, might as well make use of them right?