ooooohboy. for my island, i kind of went all over the place - i didn't have a set base plan, and i still don't. so i can definitely see where you're running into that construction annoyance.
my plaza isn't too far from my airport, and thus, it isn't too far from my beaches. as a result, i made my shop area to the left of my airport, on the ridge of beach line. nooks cranny and ables are side by side, with a little shared space in between i filled with some decorations. there's a little 'plaza' area between the two of them that i'll be using for seasonal things just to spruce things up, and make it seem more on par with the seasonal holidays (like christmas, etc.)
my villager houses are definitely all over the place. i wanted them to feel like they had their own sanctuary's, depending on their house exterior. but some of them, like olive's current location, is set up on the beach. (
ref one,
ref two - that's when Sandy was living there, but you get the idea) not all of them are placed in their "permanent" locations, however - i still have gala and hans who have houses literally smack dap in the middle of areas because i haven't moved them yet. i don't plan to keep either of them, so that's also putting a little bit of a damper on where i want to put them for now. so it's okay to take your time with figuring out everything. you might get a new villager that really inspires you to cater to them, and you could end up taking up a good chunk of space just for a personalized area for them down the road.
i have general ideas of what i want, and then i try to work them in. i never flattened my island once i got the terraforming option, so it's been a bit of a pain here and there, but in the end, i think it's pushed my creativity to broaden in how i build my island up from here on out. sometimes it's best to leave things unfinished for a few days and come back to it with a new perspective.