Against my better judgement, I marathoned the last 8 or 10 episodes, and I have no regrets. The ending was somewhat fragmented, but made sense.
One of most notable things for me was seeing the vintage KyoAni at work. Haruhi was poorly animated in many places, but it demonstrated what was attainable elsewhere. For Kanon, they tightened QA considerably. So, instead of geometry and model lapses, I complain that Shiori's hands were too big in one of the shots.
Story-wise, the 2006 M.Y. Kanon was put together extremely well. I had grave concerns about an adaptation of a game with mutualy exclusive storylines, but Fumihiko Shimo made an exceptional job letting the story to focus on each heroine in turn without having them artificially suspended.
One objection that I raised often recently was how all school romance was stupid and played out in anime. Kanon demolishies it with its raw power.
Another thing I had to consider was if Kanon violates The SDB's No Dead Girls Rule. The answer is no. Certainly, in a story dealing with death, someone has to die. But as I interpret the spirit of the rule, Kanon is not death porn (I do not watch what is commonly known to fail, like Claymore or Elfen Lied; but from recently-seen anime Attack on Titan is in a gross violation, just to give an example). So we're good.
P.S. Now I wonder just how Toei managed to screw up the material this good. I gave up on 2002 M.Y. Kanon in exasperation after some 5 episodes. No wonder someone managed to get the remake green lit. Only had to show scenes from the game to studio execs, I bet.