It's not as simple as that. There are advantages to being independent and there are advantages to being with an agency.
Being independent means running your own business and not everyone has the time and drive to do that. By your logic, every lawyer should have a private practice and not work for another firm. They keep all the money, right? But over 80% of Americans are not business owners but employees so that says the majority of people prefer to go to work, get paid, and go home. If you ever owned a business, you'd know that YOU are much more stressed out than your employees and have to deal with far more things.
An independent also doesn't make much more money than an agency and sometimes, much less (depending on your marketing skills). You keep all the money but you also lose many clients (can't respond to e-mails or take calls when you're in a session). If you hire an assistant to book and schedule, that's an added expense, in addition to renting an incall location and furnishing it (unless you only do outcalls, which brings other expenses, or work from home, which is not ideal), you have expenses that range from advertising, taking professional pictures, and little expenses like condoms, towels, KY jelly, and everything else you need during a session that a reputable agency should provide. If you rent an incall location, you are most likely signing a year lease, which means you can't take a few months off without losing that rent money. You also get clients from the agency through her referrals ("XXXX is not available, do you want to try YYYY?")
So yes, if you are willing to do more work, are business oriented and have decent marketing skills, you can potentially make more going independent. But if you want to just show up, make money, and go home, it's a lot less stress.
One is not better than the other and it's up to the girl to decide what's right for her.
As a hobbyist, I actually prefer agencies. I find that agencies are usually more professional, respond quicker, and easier to deal with. And contrary to what people think, you DO NOT get more value from going with an indie than an agency. For many years, I used Platinum Connections almost exclusively from 2001-whenever they shut down. Their girls never disappointed me, gave consistent great service, and I was never able to find the same level of quality from an indie at the same price. I didn't have to send e-mails, give references, go through bullshit... I just called M or J and said "Who's available today?".
In fact, I think many indies are overpriced compared to agencies. A lot of girls have an inflated sense of self-worth and they price themselves higher. An agency will set a rate that ensures volume.
Most importantly, indies usually spend more time on TER and its boards and more likely to manipulate reviews (asking clients not to review, offering discounts for good reviews, etc.) Agency girls usually do not give their numbers to clients while indies communicate with their clients regularly outside the bedroom, developing something closer to a friendship, making it easier for them to manipulate great reviews from them.
Look at all the indies in LA with a dozen perfect reviews. How many of you have been disappointed with one of these girls?