We are planning a trip this year and the one thing we have learned is that you need to plan and research a LOT.
I'm hearing you about it not being a park trip, so while it'll be hard for most folk here to not fall back to 'do this park too!' i'll try and balance things out a bit...
First, a couple of things to echo - if you do Disney, DisneySea should be the priority. You should still spend 2 days there minimum, but if you only have one, spend it at Sea. We have 3 weeks, and we've already put down 2 days in each park. But don't not go just because people have said you need more time there. A little time is enough to show you if those people were right, and whether you want to go back again later for a better experience.
Be prepared to be flexible. A lot of things sell out early (including express passes) and in Disney's case - vacation package guests, and then hotel guests, get first dibs on pretty much everything. A lot can be sold out so have alternative options if something isn't available.
Know the dates things are made available - As an example, Universal passes are dropped around 2 months out. Disney usually drops hotels & vacation packages 3 months out, but in our case they dropped the packages early due to the opening of fantasy springs. This sort of thing drops at a set time of day, and some of the websites drop from too much traffic \ place you in a queue. (We waited in the queue for 11 hours to secure a Fantasy Springs package, but that's not the average experience).
Even experiences like Shibuya Sky, some of the Team Lab experiences drop tickets a certain time out, and there is a rush to get all the best spots early. You might still find tickets closer to the day, but they may not be at an ideal time and you'll find yourself compromising things if you haven't planned.
ESPECIALLY because you're planning to go in Sakura season - you should get a good idea of your itinerary NOW and so that you're ready to book accommodations as soon as they're available for your dates (usually 12 months out). You'll also want to be researching all of the attractions you want to do, though with two years before you go there are going to be plenty of changes in that time, so again, be flexible)
Transport. iPhones these days can add an IC card like Suica for general public transport. If you're doing a lot of back and forth between cities, consider whether the JR pass will work, but note that it had a huge price increase last year and you really have to do a lot of long distance shinkansen to make it worthwhile.
We're hitting Tokyo, Osaka, Kyoto, Hiroshima, Miyajima, Nara, Nagoya, Hakone and then back to Tokyo, so for us it works - but if you're just hitting the golden triangle, (Tokyo, Osaka, Kyoto) it generally isn't worth it. Many of our stops don't include parks, so may be closer to the itinerary you're looking for.
Youtube is your best friend. The amount of things we've found, learned and researched by watching youtube is mind blowing. There is so much to learn, and we're still making tweaks to our itinerary based on updated info from the latest videos.
We've watched a lot of different channels, but the ones that ended up in our subs were:
For the bigger parks, TDR Explorer is really informative.
For getting around (especially as a family), Kensho Quest has been really good
For just seeing what a place \ attraction looks like without much waffle, channels like ITSUKA JAPAN provide walkthroughs
Americans documenting their travels (which is great as you learn lessons from them as a result) check out Ordinary Adventures or Tales from our Pocket
Hints and tips about everything japan from a local guy starting his own tour guide \ travel company - HARBLIFE
Hints and tips about everything japan from a local - TOKYO KENCHAN
Hints and tips about everything japan from an american guy who does travel videos everywhere - YELLOW PRODUCTIONS
Good japanese advice from a westerner (UK) living and working in japan (but mixed in with silly video collaborations made with friends - Abroad in Japan (he's also written several books under the same name)