I agree that it is best to know how to use all of the tools individually and I also know that the quality is very dependent on the great encoders that are used. But it takes all of the waiting between different parts of the process, instead of doing one process and then waiting and then doing another, it does them all back to back. You have to set all of your parameters prior and some of the stuff is simplified a bit, but that is the point. Sometimes doing it the hard way out of necessity is a good way to learn, but if they had this out a few years ago it would have made all of our lives simpler. Of course we wouldn't know as much now as we do today

.
I remember doing 2 seperate encodes to MPEG4, one with high motion and one with low motion and then editing them together. Then they came out with NanDub which did two passes by itself. Then there was the calculating bitrate thing, then everyone and his brother came out with bitrate calcs. Its part of the progress. I know how to do all of this stuff manually, it is just nice to see an app that uses some of the best codes for the job and automate it. A lot of the "all on one" apps use some really shoddy stuff. There comes a point where my time is worth a little more than just being able to say that I did it all manually. Plus with all of the newbies that are coming along, this is a nice app to refer them to.
Think of it as when computers first came out, it was a very elitest group, and lets face it, they sucked. You had to do everything manually and it took a frickin degree to use one. Now everyone and his brother has them and it is a lot easier to get around a PC. Whether we like it or not, digital video is going the same route.
So yes, it is simplified, but that isn't always a bad thing.