ATM, It looks like video acceration is better understod on the 3100/1000 than on the 6000. Even so, my 6k ran pdax, played video and games just fine. PdaXrom seems a slightly better "fit" on the clamshells, though I'm comparing rc12 on the 6 to beta1 on the 31. Basically the rom evolved on clamshells and there are a few trivial workarounds you find yourself doing on the 6k to keep up.
The 6k is ruggedized, not something to overlook,and, I believe, can pump out more juice as a usb host.
In the end, If you didn't know about these things and were handed 1 of each with no labels and no objective knowledge of the internals, told they were the same device in different form factors, and asked to play with a few apps for..say..market research, you'd find it very easy to beleive they were the same computer in different housings with different screens.
Probably, though, if you spent time comparing video performance (in a custom rom especially) youd realize the better optimization for such things on the 3100/1000. Even moving terminals around, in some cases, might make you suspicious about the differences... after a while.
As to the keyboard thing... I had a 5600 that I sold for my 6000. Had the 6000 for a little more than a year before I added my 3100. By that time I was so accustomed to the use of the 6000 thumboard that the 3100 keyboard felt oversized and slow. While holding the thing, not putting it on a table, I amstill faster with the 6000, and make fewer typos. On a table, the 3100 keyboard is ieasier for me to use.
one is not really "better" than the other imho. Get the one that has the features/price/shape strengths that suits you best.