Well... I played a dozen or so games with the Atari Logo stick and I really don't like it. I guess I've been spoiled by the Wico being in there first... I am not sure.
The throw is much further than the Wico... but the biggest problem I have is inherent with the stick design... the "notched" guide-plate. With Indiana Jones, I much prefer the "smooth" transition between directions whereas the notches on the Atari stick get in the way. The flow between directions of the Wico is much superior and I find myself getting killed by the damn bats, etc. much more with the Atari stick...
That said, the Atari stick stays... that is what is supposed to be in there... and I am sure I will eventually get used to it... but I see why people replaced them (at least in this game)... Wico's are just superior feeling sticks.