That attribution to Twain is bogus. I believe it started as a letter to the editor in some mid-20th century magazine. Let me see if I can dig up the citation.
(Edit 2: the Economist came later! see downthread)
Edit: the joke originated as a letter to the Economist in 1971: https://web.archive.org/web/20200807181810/https://lettersof.... The classic internet version (referencing the European Commission) was a later rewrite—no idea by whom. It's interesting that the original was a UK in-joke ("Haweve, sins xe Wely, xe Airiy, and xe Skots du not spik Ingliy") but the rewrite became more outward-facing, a sort of Euroskeptic joke when light humor about that was still possible (I got it in an email in the 90s), as well as quite a bit funnier.
Misassigning it to Mark Twain is not surprising, because all great quotes by obscure people get reattributed to famous writers over time. Also, Twain wrote a famous and funny essay complaining about German (https://faculty.georgetown.edu/jod/texts/twain.german.html), and he was interested in alphabet reform too (http://www.online-literature.com/twain/1322/).
First published in Astounding Science Fiction, 1946 (Astounding later become Analog). Often recirculated with accumulated changes. As far as I know, this is the original.
MEIHEM IN CE KLASRUM
by Dalton Edwards
You're right! You can tell for sure that this is an antecedent because the last line is almost the same: "his drims fainali keim tru" vs. "Ze drem [...] vil finali kum tru".
Somewhere out there is a web page tracing this joke. When I googled this yesterday, there was just a haystack of drecky results repeating the joke. But once you have two sources, you can search for them together, and that tends to bring up better results. I just did that, and probably the best one I found was this alt.usage.english thread from 1999: https://groups.google.com/forum/#!topic/alt.usage.english/iw...
Note the marvelous reply: "Thanks for your effort to clear up this ongoing mis-attribution. I remember well "Meihem in ce Klasrum" when John W Campbell Jr published it.
Btw, the author is apparently "Dolton Edwards", not Dalton, and is said to be a pseudonym (which explains the satirical "Dolt") of someone named W.K. Lessing (edit: or K.W.? http://www.isfdb.org/cgi-bin/title.cgi?57114), about whom I didn't find anything when I looked.
I thought we had discussed this on HN before, too, but all I could find was https://news.ycombinator.com/item?id=12108263, which you posted 4 years ago. Perhaps the next time this comes up, several years from now, one of us will at least find the current thread.
Thanks.
Twain did write "On the Awful German Language", on which the false atribution likely leaned strongly.
https://en.wikisource.org/wiki/A_Tramp_Abroad/Appendix_D