I don't know that butterfly effect would have made too much of a difference. Puppy would have just changed his deck around to counter it. He would have just had to rush extremely fast, which I don't think is too hard for time (If he had upped deja vu's 
) Have precogs instead of hourglasses and SoD instead of SoG. No permanents, and it gives him the advantages of knowing everything Jmizzle would be playing. Course, Jmizzle could foresee Puppy using this type of deck, and leave butterfly effect out. Or maybe added a few extras in so he could destroy all of Puppy's pillars... Or maybe he would not try and predict what Puppy would be doing at all and focused on his own strategy... All in all, I think a mono duel between these two elements is extremely entertaining.
1) Upped Deja Vus don't do that much damage, so a rush would be difficult to accomplish, especially with dissipation shield and less pillars
2) Precogs are pretty bad as a replacement hourglass, you actually don't gain any cards, you just lose time quanta to look at your opponents deck
3) Jmizzle could go for a deck-out strategy because he would know that puppychow has no eternity or procastination
But after all those reasons that you listed, you forgot the major one that would kill butterfly effect:REWIND
1) Upped Deja Vus do 4 damage for 2 quanta. I would say that is pretty effective, especially since they can be played right away if you have upped towers. Also, against an entropy deck they are creatures that would never be targeted. It would be extremely unintelligent to mutate them, and if memory serves correct entropy has no other type of creature control that can affect deja vus since they are a 2/2 and maxwell's demon does not affect them.
2) Precogs are extremely good in a smaller deck. Time has 2 other sources of drawing. Sundial, and Hourglass. Sundial would be an unintelligent choice in a mono deck, as you need to change your mark to light. Not only that, but if time was trying to do a rush, why on earth would he use sundials to slow him down? Hourglasses are a bad choice as well. At a cost of 4 to play initially, it is a cost no rush deck wants to play when it could be instead used for playing creatures.
3)
IF Any type of PvP action is all speculation. There is no way to make a deck that will be able to handle every single situation. It is just not possible, because you can never know what another player will do. You may know they have limitations, but even those are no boundary to what can happen. A particularly clever person could come up with a deck using mono entropy that no one has though of yet.
