Generations 1 and 3 happen at the same time, and gens 2 and 4 happen at the same time, 3 years after generations 1 and 3. BW happen "a few years after" generations 2 and 4, with B2W2 happening 2 years after BW.
Red starts his journey at age 11. That makes him 14 on Mt. Silver, which makes him at least 16 in B2W2. "A few years" I would most likely interpret to be 2-4. So realistically there's no way less than 6 years have passed since RBY up to BW2.
That said, I actually don't think that Looker and Anabel ending up in extremely similar situations is a coincidence at all. If anything, SM has taught me that Game Freak doesn't do coincidences. Remember a few months ago when people thought Colress would make an apparence in SM because his book had a pattern that similar to a Z-Crystal and most people, myself included, dismissed that as a mere coincidence only to be proven wrong, and that it was indeed foreshadowing? The parallels are there for a reason.
That is unless the reason Looker washed up Hoenn was because his mission to Alola
That doesn't work. He lost his memories once he got to Hoenn, and given how the UB don't actually hunt him down he's not a Faller so there's no way the Looker from SM is the same as the one in ORAS. Again, assuming the ORAS!Looker did come from an Ultra Wormhole, which is the most likely scenario IMO as nothing else would make as much sense.
Some time-travel shenanigans have definitely had to happen for this to even work out, which makes me think this will be somehow tied up in the inevitable Sinnoh remakes--whenever they come out--because it is simply way too fitting with the Time and Space Legendaries both being there. Heck, didn't Burnet say that some pokemon could potentially be undiscovered UB? If, and that is a big IF, the Sinnoh remakes do come out this generation I could totally see them retconning the creation trio as UBs, or at the very least making them somehow related.
Anyways, you're right when you say that GF made more confusing then it needed to be, but I'm a firm beliver that they'll get somewhere with it. Just dunno when.