Hello,
To be frank, you are being given a lot of half-truths combined with nonsense. It is to a certain extent busier on the trains during the cherry blossom season, but far from very crowded like during Golden Week or the end/start of the year. I've traveled during the cherry blossom season (to Kyoto, no less) and had absolutely no problem getting a seat on the unreserved cars.
If you are going to Japan next year, it is way too soon to get a pass - that is about the only true thing that was said. Once in Japan, you can reserve seats in any JR office - so there is no real wait unless you go to a main station at a busy time - not to mention if you have a seat reservation there's no wait for a seat on the train. And why would you wait at all for an unreserved seat?! What are you waiting for in the station if you are not reserving anything?? The route and time of the train departure matters also. Kyoto is a major tourist draw, but for other cities, there is far less, so again, most of what you're being told is inaccurate most of the time.
You can see regular fares, routes and schedules on Hyperdia.
Under "More Options", be sure to uncheck the Nozomi box since you can't ride that train using the pass. The schedules could change between now and a year from now, so wait til you're near your departure time to actually check.
Your travel route is very long however, so I hope you can break up your travel with several stops in between. Kyoto and Nara are obvious choices, but also Hiroshima and Miyajima are excellent, and if you have time, just a bit past Miyajima is Iwakuni with its iconic historical bridge and mountaintop castle. Plus, it's a secret cherry blossom gem with few people.
The Handayama Garden and Korakuen Garden in Okayama are some other jewels.
The Akiyoshido Limestone Cave, which is a 300 million year old limestone cave 1 km deep with an underground river and giant caverns, is also along the way and an unforgettable experience.
And Fukuoka has some must-see places too - including the Nanzoin Temple and for cherry blossoms, Maizuru Park and Nishi Park.
For Nagasaki, the best sights are the Peace Park/Museum - but if you see the one on Hiroshima you might skip it - but don't miss the Glover Garden, Dejima, Sofukuji Koshibyo Shrine and Mt Inasa at night. Gunkanjima, while it takes 3 hours, will blow your mind. It's like walking through Chernobyl without getting the radiation and dying. Try and go there first since if the seas are rough, the tours are cancelled for the day. Huis Ten Bosch and the [Sasebo Island Cruise] are also worth considering.
I think you make a good choice for your timing to see the blossoms, but remember every year is different on when they come out. From next February, you might occasionally check some forecast sites like Weathermap or the JNTO sakura page or Rurubu and if needed tweak your plans a bit to maximize your experience.
Good luck.