I posted my theories over at Hubert's place, but I think I'll share them here as well, because I have come up with a few theories as to why, I think, the older episodes and seasons are rarely shown, compared to more recent ones:
1. They're too "dated". I think Season One would be the biggest offender of this, there are hardly any computers, hardly any cell phones (though in "Arthur, World's Greatest Gleeper", Muffy accuses Arthur of gleeping her "cellULAR phone", which is pretty bulky), TVs are still relatively small and boxy, among other things. Pop-culture references would be outdated too, therefore, little kids probably wouldn't understand them.
2. Voice inconsistencies. Since like 2005 or so, the kids have had almost steady and consist-sounding voice changes (despite both Arthur and D.W. being too high for their characters), they probably think little kids are going to be confused as to why Arthur and D.W., and certain other characters sound one way one day, and another way the next. Binky, especially, had a much deeper and kind of deadpan-sounding voice in Season One.
3. Character continunity. Again, I think Binky is the biggest example of this one - throughout the entire first season, and occasionally up until "Arthur's Big Hit", he was THE school bully, all the kids avoided him and ran away from him, he came across as mean and pushy... it would probably be odd for kids to see him as a bully that every one runs away from in one episode, then see him as nice and one of the gang in another. Brain, too, is more nerdy (big comic book collector), and much more sloppy and unorganized (hates cleaning his room), which seems odd for his character today. Both Fern and George are background characters who rarely ever spoke (Fern moreso since she's far more outgoing than she used to be, while George is still shy and withdrawn), among others.
4. It may even be a case like with the Old School DVD volumes of Sesame Street, where they probably feel the older episodes are "for nostalgia", and "may not meet the educational needs of today's preschool children". Just a thought.