I thought Deception lacked an all-around good (with the exception of Liu Kang's much-needed return, of course) roster, but had a fantastic Konquest. On the other hand, I thought Deadly Alliance had an insanely strong roster, but lacked a good Konquest mode. DA's Konquest was more straight-forward and just a training session, but Deception's Konquest was as enjoyable as the Arcade mode. Between the two, I find myself playing Deadly Alliance a lot more than I do Deception. I not only find DA's roster vastly superior, but also the Arcade mode, and the Krypt in DA is insanely stacked with great bonuses. The Krypt in DA also takes a lot more time to fully unlock.
I don't really have that many complaints about Armageddon, really, and the few complaints I do have are incredibly minor. I also find myself playing the Endurance Mode (because I have the Wii version) a lot more than the Arcade, so maybe that's why I don't find myself complaining all that much. The Konquest in Armageddon is also fantastic.
I'm with you on doing away with the characters, except for Mokap, Taven, Daegon and Moloch (who I have grown to appreciate, despite being incredibly generic). I might be one of the few people who actually enjoy playing as Mokap, and I consider myself to be really good as Mokap. I like Blaze in Deadly Alliance, but not so much in Armageddon, as he looks pretty silly.