There's a lot of validity to what you say, but unfortunately this paradigm breaks because most languages are top-to-bottom.
As much as I'd love a bottom to top shell history for the reasons you describe, I'd end up scrolling in a zig-zag elevator pattern to read the command outputs.
This is of course not a criticism, just an observation.
'Languages are top to bottom', yes, but only because of the legacy mechanics of handwriting and then typewriter-rolls. (Hands or mechanism would obscure any lower text.)
As each generation spends more time with keyboarded/gestural/voice inputs for flexible screens, the old mechnical habit – append new at-bottom – will fade, with more applications embracing new-item (and new-line-insert) at-top.
Regarding shells, do you mean your eye tracking would have to zig-zag? If so, imagine a completely inverted shell/terminal, at the unit of individual lines. You'd only have to scrollbar-back in the exact same situations as in a classic terminal: when more than one screen of output resulted. And your eye tracking for smaller bursts of output will require the same reversals and vertical-magnitudes as before: just in the opposite direction. So once you habituate to the inversion, the differences that remain are:
(1) 'up' means 'newer', consistent with other screen-native scrollable information feeds
(2) your eyes' 'home row' stays near the top of your screen – closer to looking at the world above the screen, rather than the hands/keyboard/ground below
Both these seem like wins to me... far from slam-dunks, but enough to chip, chip, chip away at the traditional language practices over time.
I think what you're missing is that terminal output is nothing like the disjunct messages on twitter (and even there the inversion is terrible) but rather like the sentences of a novel.
We don't just "habituate to" reading backwards while everything else in the world still reads top-down.
And for that reason you don't break fundamental conventions like our natural reading direction that have evolved over centuries unless you have a tad bit less ridiculous justification than "looking at the world above the screen".
The next few generations will spend their entire lives reading and writing material exclusively for the screen, rather than paper. After that, I wouldn't even count on novels remaining earlier-writing-on-top. Pull-down/scroll-up for next will seem more of a 'natural reading direction' than habits based on quaint ink and paper – despite paper habits' several-thousand-years' head-start.
Let's check back in 100 years, we'll see who's right.
We've been reading top-down for well over 2000 years, since the very beginnings of writing, in almost all languages. If you really believe twitter and touchscreen-gadgets will overthrow that in not even one generation then you should absolutely share some of the kraut that you are smoking over there.
150 years ago, horse-drawn transport was the primary means of non-human-powered land transport... and had been for over 4,000 years. But by 50 years ago, not so much.
When a truly new technology arrives, things change a lot in just a few generations, with 'generation' meaning the 20-30 year average gap from birth to being a child-rearing adult.
Ok. So we have computers now, a truly new technology. And thus we will soon collectively decide that writing backwards is better because then we can look at the world above our screen better.
Yes, on second thought this is absolutely comparable to the invention of horseless carriage and makes perfect sense.
This is of course not a criticism, just an observation.