Re: Phase II and the UK
This is all leading to the Captain Britain movie. The culmination of the whole of the MCU.
In all seriousness though, I do think it all has to do with the bottom line. Follow the money. There are surely collateral benefits to shooting in the UK (unique nearby locations, for example) that would help serve whatever stories Marvel is cooking up in its movies, but I don't think anything plot-wise is actually driving the choice to film there.