Not sure if you'll be staying at the ryokans near Hakone Yumoto station. The community bus is a mini bus so it's not very convenient to bring a big suitcase along. I left mine with the hotel in Tokyo when I stayed in Hakone.
I compare between SQ (noon flight, landed 9pm night) and Scoot pricing (Midnight flight landed 11am) and timing and thinking of booking scoots as it save me a day. Althought SQ Haneda & Scoots Narita.
So I thinking of heading straight to Gotemba and spend a night there and next morning to Hakone before returning back to Tokyo.
Below are some possibility I'm thinking of...
1. Check in Tokyo and check out the next day and deposit my luggage in the hotel for one night if they allowed.
2. deposit in locker for 1 day.
3. check in Gotemba or Hakone on day 1 from Narita and spend the remaining day in Premium outlet. Next day deposit luggage at hotel and head for Hakone and collect at the end of the day...
Day 1 is unlikely for Hakone tour as I reached there most probably late noon..
Oh ya, I read about this hotel named Fujiya.
It's between Odawara & Gotemba with approx 30mins bus ride, should be good i guess?