1. The "forbidden love" plot between Marsala and the blonde girl was abandoned.
2. The neos were clearly better armed, more capable, and more intelligent than the terrans. In the second season they seem to claim they're superior, yet make bungling moves at every opportunity, and literally cannot win a fight to save their lives.
3. There are way more plot holes in season 2.
That said, there are some great moments here; Thrax' sacrifice to save the men under his command, hints of complexity in Phaeton's character, etc.