Help with itinerary: Tokyo to south/reverse?

Hello, I try to plan itinerary for first timers in Japan. we will travel around a month from late March (around 27th) to late April. We will land and departe from Tokyo.

Tokyo- 7 days (includind day trips to Nikko and Kamakura)
Ise- Half a day
Nagoya- 2.5 days (includind day trip to Inuyama)
Takayama- 2 days
Kanazawa - 1.5 or 2 days
Kyoto- 6.5 days (includind day trip to Nara and half day at Himeji)
Koyasan (Mount koya)- 1.5 days
Osaka- 2.5 days
Hiroshima- Half a day
Miyajima- Half a day
Nagasaki- 1.5 days
Kagoshima- 1/1.5 days
Yakushima- 2 days
Kumamoto- 1 day
Takachiho- 1 day
And then a trip back to Tokyo.

Or to do it backwards, and take a domestick flight from Tokyo to south and then travel up to Tokyo.
considering the weather and that's in the end of April there is a golden week, what would you recommend as the better choice?

Thank you :)

You seem to have a decent trip sorted out.

Re going one-way: flying from southern Kyushu to Tokyo takes under 2 hrs, whereas train takes over 12 hrs. You can fly from either Kumamoto or Kagoshima, if you put one of these places at the end of your trip. There are low-cost carriers (not sure if any of them fly these routes - you'll need to check), or you can do one of the 10,800 yen deals from ANA or JAL.

You may find that (depending on who you fly to Japan with), you can get a good deal flying straight to Kyushu (with a change of planes in Tokyo, but not needing to leave the airport), and flying back from Tokyo.

However, depending on whether you get a rail pass (I assume you will for such a long trip) and what length of pass works out best for you, you may decide to take the return long train journey as a money-saving measure. If you do this, you may want to do the whole return journey in one day, or perhaps you may want to take two or three days and visit some of your destinations on the way back instead of all in a straight line.

Golden week will be busier than normal weeks (and hotel rooms will be more expensive/harder to find), so you may wish, for example to spend Golden week in Kyushu and visit Kyoto/Koyasan outside of Golden Week. Someone else may be able to tell you whether Tokyo is busier or quieter in Golden Week (i.e. do more people leave Tokyo for the country than come into Tokyo for a city break?)

Thank you :D

As you are travelling for longer than the standard railpasses, you might also want to consider breaking up your itinerary into a non-linear one and flying some of the longer distances on the ANA/ JAL tourist fees and covering certain areas by local JR passes (i.e. Kyushu) - fly to Kagoshima and work your way up north.
Remember that Nagasaki is not connected to Shinkansen and needs extra travel time compared to other destinations.
I find the museum in Hiroshima quite harrowing and would probably consider some extra time there to get through it. Half a day might rush it.

I think you have too long in places with your long stays, and not enough time in some of the other places you have marked as 1/2 days. Also, check the travel times - places like Nagasaki take time to get to and back-track from. Ise might be another one (it's a bit different to some of the other locations), and while technically possible it is not a 1/2 day, a full day from somewhere like Nagoya or Osaka.

You also have a very city-centric trip planned with what I consider to be significant double-ups while skipping other interesting places. You could easily take Kyushu at a slightly slower pace and get more out of that part of the trip. However, it is your trip, and that might be what you are interested in.

Hello, I think that add another domestic flight just burden our budget, we try to make it as cheap as possible and the mess with go to and from airport and the cost of it not worth it.

About the local JR pass, its a good idea I will check it :)

I know the way to Nagasaki is a long one and adjust the itinerary with the hours its take to get to each place(and add days when necessery).
I change the travel to Ise as a day trip from Nagoya. I read from couples of people that they did it and it was enought time there (it's only 1.5 hours from Nagoya.
I also took off some days from long stay in one place, and add it to places with not enough. it's still busy but better lol

Thanks again to all! ^_^