I did some poking around the Fluid and D&D sites, and I found out some interesting things. It is possible (though non-trivial) to create custom classes using Micro$oft Access; unfortunately, the copy of Access I have is from 1997 or so, and can't open the files. There are a couple of fan projects underway to create a Class Editor. Once one of those is available, that will take care of most of my big complaints.
The main interesting thing I have found, however, is the sheer number of odd workarounds that E-Tools is requiring. All of the various types of dragons are only given stats for the "Adult" category, for instance ... if you want to create Hatchling, Young, Mature, Old, or Ancient dragons, you have to go through a pretty complex process.
Simple magic weapons (say a +1 longsword or a wand of magic missiles) have to be created on an "as needed" basis and added to the item database. Again, not hard to do by any stretch of the imagination ... but still something that seems awfully non-utilitarian in what is supposed to be a software utility.
I don't want to bash the makers of the software too much ... this is a complex project they've taken on, and a lot of precious budget and effort was wasted early on in a misguided attempt to make some sort of Neverwinter Nights-ish product instead of just a good DM tool, which is what people actually wanted. But it must be said, that E-Tools is only half-baked. I paid $30, and at the end of the day, am ending up doing a lot of the same work I'd have to do on paper with the hardcover books I already own.
It's fixable; but that it needs to be fixed, is disappointing at best.