How much time are you planning to spend there? Are you more space conscious or are you guys ok with the typical Japanese sized rooms and beds? Their "double bed" is not the same size as Queen in the US and the room that they say "can sleep 6" are more likely a 2 person room for the "typical" 5'11" American with BMI of 27. I personally always stay in their business hotels like Toyoko Inn but if you are a tall and big American you can easily bump into places left and right. My ex-wife is 5'6" and she felt claustrophobic in their bathrooms. I am perfectly fine as a 5'9" but I grew up in the most crowded city on earth so everything is fine by me.
I've only been there twice but I am always the over protective and safety margin conscious kind of person so just take my advice with a grain of salt. Transportation transfer can be a problem if you are relying on switching trains between different companies. Unlike many countries where their train systems are owned and run by a central transport agency, they are mostly privately or regional owned and don't like to direct passengers between transfers of other companies and would actively not display signs in between. So if you can transfer within the same company's trains, even if it may look like 30 mins longer do it, you will miss your train if you try to transfer relying on Google Map or Apple Map, you won't run in between fast enough unless you do it every day.
Also do take the dedicated trains for airport transit instead of hopping onto the local train for commuters, they may not yell at you but everyone would not like you for doing the "wrong thing" in their customs. If you got stuck there are train station staff you can ask for help but don't ask strangers or shops, they don't like that too much (except maybe convenient store clerks who may often be foreigners who know English).
If you start by landing in Tokyo, get the Suica card when you land and use it for everything, or you can install the Suica app on your phone. It is much easier to use those cards than cash (you may miss a train or a bus). The app system is helpful that you don't need to worry about returning for deposit etc, but you have to keep track of your battery life. Speaking of battery life Charge Spot is great if you are low on battery during the day. DO NOT CHARGE YOUR PHONE AT A RESTAURANT. That would be considered stealing electricity there (I know it is petty but that's their custom), so don't do it.
Luggage storage locker is great but get full very fast and early in the day. If you run into luggage storage issue during the day, and you don't want to detour to your hotel, Bounce app is great finding a spot you can temporarily store your luggage so you don't have to haul them around. It once point me to a karaoke during day time when it is just running as a luggage storage. Very helpful even if it cost a few hundred yens.
Wait time for famous restaurant is very dynamic. Just because they typically say 30 mins doesn't mean the day you visit is 30 mins, it can be 1hr 30mins. Make sure you have some flexibility. Some of them don't open every day and they close early if they sold out. Some just don't take foreigners like in English they say they are closed but if you can read the Hiragana they are actually open etc. Don't take it too personally, you'll get used to it. Many of them don't do take out, and most of them don't let you doggy bag like the US restaurant, but they are often ok if you order a little then order more to be safe. Some don't like you not finishing your food (it is disrespectful to the chef) but as a foreigner they may forgive you on that.
As always remember to dial down the politeness by a few degree to interpret their real meaning. If they say it is a bit difficult it literally mean they don't like it. When they say it is checkout at 11:00 they will charge you a thousand yen if you are off by even 2 mins, they are very precise on time in culture.
As to spending more time where, it is all about what you like. You will get different opinion from different people but I personally think in one trip you will likely not have enough time for all 3 places anyways. You can always book places with free cancellation and change your plan as long as you cancel early enough.