Hmmm... I'm going to stick my opinion in and comment on the original questions posted...
Linux is perhaps MORE transparent than Amiga, simply because it's Open Source. The converse to this is that, of course, it's slightly more complicated.
It's powerful, multi-tasking, works with most hardware, and the software components have been tried and tested over years - the core utils are tight and elegant.
The directory structure makes sense just as much as the Amiga's. Just remember that Unix and Linux are multi-user; that's why you get directories like /bin /sbin /usr/bin /usr/sbin, etc.
The major distros are extremely complex, and that includes Ubuntu. But not many people realise that all that's needed to get a completely functional DOS-style command line up and running is a working kernel (compiled specifically for your hardware), and a few core commands, libraries and devices. Literally a few MB! And surprisingly easy to do.
I've seen an entire console-based system take up less than 128MB: wordprocessor, database, spreadsheet, email, web browser (with graphics and JavaScript!), instant messenger, mp3 player, CD and DVD player (yes, running in the console!), picture and PDF viewer, games and utilities...
After that you can add a cut-down version of Xorg and a simple window manager, and you've got a functional GUI. (There are many, many window managers, from ultra-simple, mouseless jobs like RatPoison and Ion, to behemoths like KDE and Gnome.)
But the best way to learn Linux (and realise that it's not really that far distant from Amiga) is to build it yourself. Try Gentoo or Linux-from-Scratch and get your hands dirty by putting together a minimal system (there are a few how-tos out there). Linux can be as simple or as complex as you want it to be. If you want efficiency and elegance, do it yourself. I've never come across another OS that gives you so much choice!
