The sad thing, though, is that apparently a lot of people must have accepted the anime's ending. Because, there is no way for them to animate the rest of the manga's story as a continuation of where the anime left off, simply because the ending that they made-up would completely conflict with the rest of the manga's story line. They could choose to ignore it, but people who haven't read the manga would then be lost and confused as hell as to how Onizuka would be back to teaching after being chased out of Japan by the cops. The only other way to animate the rest of the manga would be to start the series from scratch, either through new animation, or using the old animated episodes up to episode 41, and then contiuing on from there with new animation (completely skipping/ignoring the non-canon ending).
Personally, I wouldn't mind if an animation studio went by the 2nd option, but either way, the anime's ending really seems to have screwed up any real chances for the rest of the series to be properly animated. That's really a shame, because the Mayu, Rescue Urumi, and Teshigawara arcs are some big highlights of the series, for me. Not to mention thatthe last arc senRAB the series out with a bang, itself, IMO.
But, still, even with the anime's abrupt ending, I still love the enjoyment that the first 41 episodes of it brought to me, and even those alone are still good enough to make GTO one of my favorite anime.