I always thought that the inclusion of Din, Nayru and Farore in Minish Cap was basically just an easter egg, a nice reference to the Oracles games since they and Minish Cap were made by Flagship. The idea that they are either immortal or that their names are passed down through the generations is nice too. I think I prefer passing down the names, personally.
As for the castle, perhaps it's not that the Minish Cap castle resembles A Link To The Past's, maybe A Link To The Past's resembles Minish Cap's. Allow me to explain.
The Minish Cap is set in a time of great peace and prosperity for Hyrule (until Vaati comes and messes it up). Well, further down the timeline we have Ganon destory Hyrule Castle in Ocarina of Time and then defeat the Hero. He is sealed away but this leads ot the Imprisoning War, after which there is another period of peace when Hyrule Castle would no doubt be rebuilt.
Perhaps the newly rebuilt castle we saw in A Link To The Past was designed similarly to the one from Minish Cap to echo that peaceful period of Hyrule's history.
Speculation aside, I agree with Beauts and SpartanGibbles. The design of the castle was most likely just a way of tying Minish Cap to A Link To The Past aesthetically. Maybe this was to give a sense of nostlagia to older gamers. Maybe it was to create a stronger connection between Four Swords which was released with A Link To The Past on GBA.