Yes, Season 2's ending was strange......but I still apprecitaed it, since I had to fight tooth and nail for it to be broadcast!
For some reason the channel that broadcast it stopped 10 episodes before the end of season 2, and went straight into season 3. So I joined the general outcry that was going up, and joined one of the many petitions going around the site.....plus, I sent in letters. So, because it took so much effort to finally get to see the last few episodes (and at Christmas - yay!) I truly still love them...even the last one.
Season 2....I loved the Darkness Before Dawn (Wormmon's death) and the one where Ken was in a self-inflicted coma. After that, I just loved all episodes where angsty Ken had centre stage...like at certain points during the Isect Master's House episodes, or when he went in the van to 'help' the children, who were being held as 'hostages'.