My past two trips were Copper Creek and Fort Wilderness Cabin, so I'll chime in!
After staying deluxe for the past few years, I was admittedly worried about doing the cabin. I got used to having so many amenities at my fingertips. However, I absolutely LOVED staying in the cabin and would do so again.
At Copper Creek, we stayed in a studio room so I don't have experience in a 1 bedroom villa (though I did snag one of the few secret larger studios. only 2 on each floor!). The CC rooms are very comfortable and well designed. Its a room you will enjoy spending time in. A big plus here would be the king mattress I believe those 1 bed villas have, in a separate room (vs the queen in the cabins). And since it is a deluxe single building resort, many of the amenities are close at hand (transportation, dining, comfy lobby, pool, etc).
Now the cabins: they were all recently renovated and look and feel amazing. The furnishings are differently styled/colored, but honestly the counters, faucets, and other finishing were the same high end type as CC. Its a beautiful space. I stayed in one w/ 5 people and we had enough room, though coordinating morning showers took some planning. With just a party of 3 you will be more than fine, and someone could even take the pull out couch if they want a separate sleeping arrangement. It really is surprising how roomy they feel, and you get a full kitchen (plus charcoal grill and a porch) for MUCH cheaper than CC. The cabins are an entirely different experience than a normal resort, and I must say I fell in love with it b/c it feels so unique from any other stay. You really feel like you escape somewhere. The main difference in vacation style that they require, is that you must allot slightly more time than usual for transportation (since you cant just take an elevator downstairs to the bus stop). This is why I recommend getting a golf cart for your cabin stay. It's incredibly fun (honestly my favorite memories of the trip were driving the cart around) and allows you to not wait for internal buses, make your own easy schedule for getting to the resort buses or marina, or if you need to shoot over to a pool or store quick. Even with this added expense, it should still offer you plenty of savings from a CC stay. And don't forget there are resort loop boats to take you to WL and Contemporary, so you can still do Chef Mickeys and Whispering Canyon (I also recommend relaxing at Geyser Point!).
If you do not wish to rent a golf cart, Id recommend requesting a cabin close to the pool or a bus stop. ...but you should totally get a golf cart. its part of the experience. thank me later! ;-)
If pools are important to you, WL absolutely has better pools than Fort Wilderness. (I may not be the best judge though since the main pool at every resort is too crazy and hectic for me to step foot in, I only do the quite pools. the cabin quiet pool is extremely basic, but indeed very quiet. so that's all I needed. WL has much more themeing going on.) As for allergies, no one in my party had any. But the cabin was spotless and I know they take those deep cleans seriously when requested. Anecdotally, I didnt see anyone at a cabin with a dog during my stay (the few dogs I saw were with folks staying at the RV campgrounds).
All in all, I'm an impatient city boy who was used to staying at deluxe resorts (Contemporary, Poly, Copper Creek) but after having so much fun at the cabins and seeing how much money I could save, I'm ready to go back in a heartbeat.