I watched a couple of episodes of NieA_7 back to back with some Lucky Star, and the contrast was quite striking. I haven't seen the 2006 Kanon, but it's clear that KyotoAni know their stuff.

I mean, you just look at these confining lines! Not only drawing in Lucky Star is better, but the motion is more flowing and natural.

Budget? Maybe it's a part of it. Although, I think it's not just just the budget. Hidamari Sketch is also animated better than NieA_7 (wherever animators bothered to do it).

I wish the whole of Lucky Star were made like the few "superpainted" moments, but even as it is it's great.