I do sometimes get confused about the different web readers, but I like to use them all l because:
a) HandStory is great for on-the-fly work and brilliant for images (in my case, mainly maps)

Plucker lets you produce files that can be launched from the launcher
c) iSilo is the only one that can handle tables, though not very satisfactorily - I find it's very slow to move around within the table. I'm only just getting to know iSilo and may make more use of it. Certainly, the ability to select and copy text is useful, and the autoscroll is pretty good.
One advantage of using more than one web reader is that you can switch between different documents simply by switching between the different applications.
As regards AvantGo, I guess you're right. I've just been too lazy to convert the sites to Plucker or iSilo, and like the convenence of the automatic update on each hot sync, but the application does take up rather a lot of RAM, so I'll probably ditch it soon.