I am very, very happy to see this project back, a nice little welcome home present :)
Going from what I learned over the course of the last CTP project this first pick is going to be having a hard time by the end of the project, unless we do for for something that can always do its job, and well. This is the beginning of a long project, so we obviously don't want to start to limit anything straight away. I feel that picking something now that is either more defensively orientated or perhaps a decent offensive threat, rather than serious powerhouse, may sort of come back to bite the team in the ass in the latter stages of the project. As ganj4 mentioned in the OP the last pick for team 1, Deoxys, really did tilt the scales in favour of team 1. That said I think what would really be a good way to start off team 1 is a nice little offensive powerhouse that sets up, but does not require a set up to still do damage.
In my opinion the three optimum things for this would be SD TechniLoom, SubSalac Terrakion and SD Lucario. I'm glad to see that all 3 of these have already been nominated because I think they provide a great footing for the team. I may be slightly more inclined towards Breloom then Lucario, and Terrakion last because of the different levels of versatility, for instance Terrakion is an amazing user of a Scarf or Band as well, and if either was needed in a 5 or 6 slot and SubSalac was already selected then there may be issues. I personally believe SD TechniLoom is Breloom's best set in this current metagame because of how much it can threaten, and how quickly it can do it. On all my HO teams I have a Techniloom, and I will often switch to it after my lead. I tend to be able to knock out anywhere from 2-4 things with it alone, provided my opponent doesn't have a Xatu/Espeon waiting in the wings.
While there are a few things that can easily dismantle teams from the get-go, I believe TechniLoom also provides a great building block to start with. TechniLoom's counters are all known, and if you aren't packing at least a check to it, you will be saying goodbye to half your team. That means that from team member #1 we can already dictate a member or two of team two, even if its at the #6 slot. I won't make a nomination because TechniLoom as already been nominated, thats just my justification as to why I believe its the correct choice for the first member of team one, I would personally go with the Life Orb over Fight Gem, as it really facilitates Loom's early-mid-late game sweeps.
Credit to Gengarnemisis for the submission.