I've never punted with an agency so take what I say with a pinch of salt, I considered it for my 4th ever punt when I started out and back then I did a lot more research before organising a punt. The following is a basic summary of what I found on here and on the agency sites themselves.
In general the differences between independents/what you might expect from agencies and agencies themselves are the following:
1) Agencies tend to Photoshop more and have better people up to the task so it isn't always obvious.
2) They, especially the dodgy ones of course, tend to bait and switch more often than independents.
3) There are agencies that are 100% dodgy with B&S's and there are ones that are 100% legit however some are somewhere in between with a handful of genuine girls that they use for the switching but who are also featured on the site anyway. For those you wouldn't know if the agency was dodgy if you got lucky by asking for one of their genuine escorts, there is plenty of info on the punting wiki that you can get to from UKP which you should definitely read up on.
4) As you probably noticed the pricing models tend to be very different.
5) The reviews on agency sites are even more likely to be full of shit than the ones on AW. I would strongly advise against listening to any of them and instead you should only go with the WG's and more importantly the agencies reviewed on here.
6) Agency girls are more likely to have drivers/bodyguards. In the event of a bait and switch you could get threatened by one of them and forced to fork over some cash to "cover" the cost of them coming out to visit you (if it's an outcall, incall ones are obviously more reliably) while threatening you. If it's a legit escort then no worries even if they have one and the escort i'm guessing would feel more at ease during the booking.
That's all I have, best of luck.