An indy girl can set her own schedule, of course, but that doesn't guarantee "freshness" (with well reviewed girls, it usually does).  An indy girl controls 100% of the fee.

There is an unverified belief that the agency books appointments and the agency girl follows thru.  If they book ten guys in ten hours, she has to see them.  The agency girl gets around 50% of the fee and turns over the rest to the agency.

Personally, I don't believe that agency girls can't tell the agency that they can't see 10 guys or even 2 guys in rapid succession.  

A girl that is desperate for cash, indy or agency, will book as many clients as possible while she has her hotel room (to maximize her ROI).  A girl that is too tired or needs more time to freshen up should tell her agency that she is behind schedule or can't keep up or needs a break.  I know that I've been delayed for many agency in-calls ("She's running late ... another 10 minutes." which usually turns into "30 minutes" or more.)  A bad session due to overwork will make a bad impression for that agency - penny wise, pound foolish, so to speak.  But not all indy girls are good at sticking to their schedules.  

I've seen indy girls and agency girls.  No major downside to seeing the agency girls; sometimes the ADDED CONVENIENCE of being able to talk to the phone girl and not having to worry about reaching the indy girl while she's shopping, at a movie or otherwise engaged.  

I've been NCNSed too many times and, with one exception, always by indies.  The agency phone girl is or should be always available.  (I stopped using an agency that OKed me at T minus 1 hour and then suddenly wouldn't answer my emails with the final info / room number.)  

Let the reviews be your guide to specific indies and agencies