One, the DVDs were pressed before the episodes aired on Toon Network so they would have to push back the release date to get them on there.
Two, more money. And more promotion of the third season. Seasons 1 & 2 came out relatively close together on TV. People who saw s1 could remember it well enough when s2 started. However, wasn't it almost a year before s3 came out? A little reminder of all that happened was a good idea. Hence the DVD. Plus they get more money because people will buy the first DVD and then have to buy the second. But, knowing Luca$, he will also subsequently release an edition with all three seasons spliced together contiguously, heretofore pissing off those of us who already bought s1.