First off, congratulations on planning a Yosemite honeymoon. What a great idea. You've gotten some very good suggestions. Here are some other ideas are you.
Re: hotel
Ahwahnee is very nice. The ~$500/night per room you pay is for the location and the historic lodge. I have only stayed there once and the room was not that special. I think the cottages may be nicer. But on the rooms, 232 and 234 have a middle suite living room that is quite nice. These rooms sit above the solarium. You can try for one of those and the adjoining living room. They also have four or five special suites on the 4th and 5th floors. But for me, $500/night is quite a bit of money, if it's not for you, definitely go for it. I actually have found that Ahwahnee is usually easier to book than the lodge, at least it often has showed availability when I have looked. But for me again, one of the beauties of the Ahwahnee is the great rooms, which anyone can enjoy. Have one meal in the dining room. Have low expectations for food and just enjoy the ambience.
Yosemite lodge - this is your standard hotel room, running around $150-$250 a night, depending on season. A safe bet.
Curry Cabins
with Bath - these are my favorite Yosemite lodging options that I can afford.
Around $200-$220 a night. Because I have the convenience of my own bathroom and shower, but still in Curry Village, and you can sit on the porch and not be surrounded by cars. Make note that the Curry cabins without bath IMHO are worthless. I like Stoneman house too. Curry also has a 'specialty cabin', you need to call and ask for it, but it's a bigger cabin with a living room.
Re: Hiking
If I had 3 days in Yosemite, I would take one day and drive up to the high-country, if it was not raining or snowing. Sure, the meadows are brown, but it's so beautiful up there, and you'll be able to enjoy solitude on the hikes. If you're just making a day trip, hike to Gaylor/Granite lakes for some gorgeous scenery. Two other day hikes that I think are fabulous are Mt. Dana and Mt. Hoffman. -I- would not try either without spending one night at elevation to acclimatize, but everyone is different. Mt. Dana will give you some amazing views.
Re: cute places around there, you didn't say which direction you are driving from/to.
Finally, Yosemite is always beautiful but note that you are traveling late October when the falls won't have much water. Yosemite falls may be dry. If you're lucky, there has been at least one rainfall to wash away some of the dust.
Congrats again!