After experiences on the ladder with teams such as yours, I have begun to reconsider option 3. I was heavy option 2 from the start, but short Scoli chains have proven to be rather dangerous on their own. I am now beginning to lean slightly toward option 3, although would be quite happy with either. I'll await more discussion and perhaps ladder more before voting occurs so I can be sure which to vote for.
Let me just start off by saying that in no way am I saying that those replays and that general idea of a short BP chain is not good or possibly problematic. I am, however, saying that what the shorter chains are capable of doing to a game is in now way comparable to the standard BP chain. Looking at the replays, the first thing I want to say is congrats on winning those, the deck was stacked against you quite a bit. After that, I would like to note how much easier it is to counter the BP portion of the team, which I am assuming is Scolipede, Espeon and possibly Togekiss. Between the two/three of them, they don't exactly have amazing synergy in terms of taking attacks for one another, especially without accumulated defensive boosts.
More importantly though, I find the fact that some part of the chain may have to pass boosts to a dead-end otherwise else risk getting KOed to be the most important difference between the two chains. With a full Baton Pass team, you can just pass over to someone who can soak up an attack, set up while the opponent switches and then pass again if necessary, never really slowing down your momentum. On top of that, with 6 Pokemon in the chain, you have many more ways to accumulate the necessary boosts. On the other hand, with a three-Pokemon chain, you have fewer ways to accumulate boosts that can be passed on while also being faced with more ways to slow down your momentum. Obviously, the momentum isn't lost because you will be passing boosts that can be utilized, possibly built on, but just not passed. Although this seems to be irrelevant in the face of some Pokemon with a +12, it actually opens up more options to get rid of those boosts. Without defensive boosts, which will be more difficult to build up (although Iron Defense Scolipede is still going to be annoyingly efficient), having your opponent survive an attack will potentially be much more devastating than it would be in a standard BP team. On top of that, phazing will be easier to pull off, especially/primarily late game, when the boosts reside at a dead end. Unaware users now have much more value with Espeon being out of the question if the boosts have been forced onto a Pokemon outside of the chain.
Essentially, what I am trying to say is that having fewer Baton Pass Pokemon are much more manageable because there are fewer ways to accumulate boosts. On top of that, the defensive synergy within the chain itself is far less solid than in a standard chain. This makes it much easier to force the boosts to a dead-end Pokemon, which then allow for phazers/Unaware users/anything that isn't getting OHKOed to have a window of opportunity that can be utilized. Obviously the number of counters isn't vastly greater, but
the fact that the person facing the BP team isn't simply helplessly watching boosts build up and instead can apply pressure to force the opponent to cut off their momentum building prematurely makes it much easier/possible to play against without counter teaming.
I am completely open to any arguments in favor of option 3, especially since those replays raised my eyebrows. As of now though, it seems like option 2 sufficiently turns the battle back into an interaction between two people rather than one person stacking boosts while the other guy watches.