I think it is really difficult to create content like this in a "one fits all" way, given differences in how various regions approach it. BA is a novel concept within XIV, and we see how it highlights differences in style which are hard to bridge if sticking with the current format -- if anything I want to hand the devs some aspirin as they have to deal with this kind of headache now.
Something I noticed though beyond the issue of portals/PUGs vs DF/PF, and while playing on Aether (no idea if the same issue exists on other datacenters) is a general problem with the fact that BA is directly linked into Hydatos instances. Once people enter BA suddenly up to 56 people are gone from the instance, and prepping any high-level NMs becomes even more difficult than it is anyway, given a good chunk of the Eureka population is sitting by default at base semi-afking and waiting for NMs (hopefully) spawned by others to pop. Remove 1/3 to half of the instance into BA on top of that and... well, yeah, you get the picture.
I just came out of an instance and there was exactly ONE group prepping the dragon, and just getting this single party together took an incredible amount of cajoling. You can imagine how long that entire effort to spawn PW took... X_x (but at least it popped, while I have spent more hours than I want to count on fruitlessly trying to get a prep for high-level NMs in Hydatos going in any meaningful way...)
Therefore I think a direct link between Hydatos and BA is a bit on the problematic side to begin with (at least on NA servers? idk...), but given there is the entire thing with the support FATE I see no real way how to address this issue now. If anything it might be something to consider for future content of this kind -- depriving an instance hinging on plenty of players doing things of... well, active players by sending them to another instance can cause unintended problems.
That aside, and something which might alleviate at least some of the problems for NA could be a system which allows premades to chose what instance they enter (Hydatos 1, Hydatos 2, Hydatos 3 etc.) -- that way quite a bit of stress and hassle would be removed from the picture. Combining this with a clear labeling of "Arsenal" instances vs. normal Eureka instances could also be an idea, so that people who want to specifically enter BA, and/or do the support FATE there could enter Arsenal-instances (and as 56-man premades all but hog or even "create" such an instance, thus also less bickering about portals on NA servers), while those who do not wish to see their efforts to prep high-level NMs hindered by suddenly "losing" up to 56 players to Arsenal go to "pure" Eureka instances. I just worry a bit about that approach, as it could leave one or the other type nearly drying up... >.>