To some extent it depends on how you learn.
In practice, most people take lessons from whichever rink is most convenient - and most rinks only teach one organization's group lessons. For most beginners, traveling to a distant rink makes no sense. On top of that, the match between your learning style and the teaching style of the coach often matters more than exactly what is taught.
Almost everyone needs to learn from a coach who is good at both demonstrating and explaining, at least in part. But a lot of us adults can't learn well unless we can read about the skills too, and watch videos.
ISI sells to its members (and membership is cheap) a fairly complete
Handbook and
DVD. So if you are to some extent into self-study, that helps.
USFSA (also called USFS) doesn't sell much of anything useful to skaters, and even the "Basic Skill Instructor's Manual" has this skating season become largely useless (because they no longer explain how to do most skills), though it used to be more useful. Their Basic Skills DVD is somewhat useful. Toth the manual and the DVD are only available to registered Basic Skills instructors. The USFSA has a lot of technical information on the WWW useful to people who want to stay eligible to compete within USFSA and ISU, but relatively little that is particularly useful to skaters - and the few words that are useful, are stuffed in the middle of 10's or 100's of thousands of words about maintaining eligibility, and other rules having little to do with how to skate.
To me that makes ISI's methodology overwhelmingly better than USFSA. But if you don't learn that way, it may not matter.
The intro USFSA sets of classes are about learning skills like "Marching" which have nothing to do with skating. If you start with ISI alpha level skating, your first lesson with ISI will include skating, which is, quite frankly, scarcely more difficult to learn than trying to march on the ice. Even if you choose the slow route, and start with "ISI pre-alpha", you won't waste time learning to march. ISI pretty much immediately starts off with real skating skills, though both USFSA and ISI . USFSA tries to justify its slow start-up in terms of getting people to understand the idea of shifting your weight from foot to foot, and understanding what uses edges means - but most USFSA coaches don't actually explain those things in their group lessons, so the very slow startup seem pointless.
As an adult, you may find learning with kids a bit frustrating, and may prefer the adult classes, though at most rinks, adult classes span a fairly large range of customer skill levels. And both ISI and USFSA lessons were really crafted for the learning styles of kids, even if you take the adult classes, in the sense that they assume you have a very short attention span - so instead of learning one skill at a time until you master it, like you would in PSIA ski lessons, which are much better organized, they shove a whole bunch of skills at the class, spending 2 - 4 three minutes total / skill / class, which also means that instructors spend more time babysitting and entertaining the customers than teaching. They repeat the same bunch of skills every week, never covering the skills in sufficient detail to really understand them. In addition, the nominal teaching styles of both organizations are aimed at "monkey-see, monkey-do" learning styles, without much explanation, which style works for some people, especially young children and some dancers, but which works less well for many adults. Those issues are part of why the self-study issue is important to some of us, and the availability of that is so much a part of why I think ISI is better.
I stopped taking private lessons for various reasons, mostly economic. I'm taking a group lesson adult class, taught by my most recent private coach, whose teaching style I like a lot. There are 5-6 people in each class - pretty small, and she tries to spend a few minutes with each student, in part because the class spans such a range of skill levels. But she has so little time to teach each student, that it is very frustrating. She doesn't really have time to spend analyzing each student's issues. Group lessons make a lot of economic sense, but if you can afford it, private lessons from a really good coach who teaches in the style that you learn best are a lot more efficient use of your time.
Hope that helps.
As you can see from the responses, I'm prejudiced towards ISI - but not everyone agrees.