Cinema, Yes, not running DCE is a liability in most cases, but the great thing is in BW-On you can still tech Sableye because people will be too scared to start a Mewtwo war, especially with Sigilyph running about.
The intention with Mewtwo versus Darkrai is not to OHKO, although that is a bonus. The real intent with aggro Mewtwo vs. Darkrai is 2HKOing, because even the Darkrai player can't OHKO you, so a prize trade is viable.
Cinema, Thundurus is a great card in BW-On, but I think you'll like Page 3 of the Mewtwo/Zekrom/Eels discussion thread, a lot of people agree with me on the Mewtwo start in HGSS-On. http://www.pokebeach.com/forums/thread-the-mewtwo-ex-eelektrik-zekrom-discussion-thread?page=3&highlight=Mewtwo+EX+Discussion
Cinema, T2 80, T1 40. I can consistenly get T1 and T2 DCE so that isn't a problem. Starting a mewtwo war is always a good thing since you run more than th and of they ran more than you like CM they were going to start it anyway. T2 120 with room to survive a couple hits in comparison to Thundurus and actual usefulness in the late game is a lot stronger than T2 80.
It's a very subjective opinion, what is the best starter in Eels. Some say it's Mewtwo. Some dislike the fact it's a free two prizes T3 or so. It can get T2 120 (DCE) 40 firs turn. Thundurus is nice, but it always has issues with space. T2 80 isn't so powerful of you can't even get it though, T1 Darkrai D Claw, however unlikely and situational that is. There are just better ways of dealing damage and discarding energy T2 (Junk Arm, T2 Zekrom, Ultra Ball, Juniper).
Smeargle WAS the best starter in all decks including ZekEels. It's gone now though, so the best starters are Sableye or Mewtwo. Thundurus is really an outclassed card.