Hi there
I always bring people go hakone.. I would suggest u to always catch a romance car between 9 to 9.30 am. then follow this route:
1. stop at hakone yumoto. take H bus to Moto Hakoneko
2. Have nice lunch at the many restaurants there. Tempura rice set mindblowing.
3. board the Pirate cruise ship from the Pier there. Walking distance from restaurants there and can see a big ass Shrine-ish gate
4. Get down at Togendai ko. Board the ropeway until Ubako station.
5. Ride cable car to Sounzan or Gora.
6. Take bus/touzan line back to hakone yumoto.
should finish like at 5pm

If want earlier, then try boarding the 8am romance car.
oh and yeah.. go buy the hakone free pass at 5,140 yen! If u dont take the romance car, then just take the odakyu railway until hakone yumoto. and can return using the same pass.
so quite value for money.
EDIT: eh u staying in hakone itself isit? pretty sure u wont drag until 6pm at all then.. dont have to take tozan line le.. i tink the best ones there are only the cruise ship and ropeway. others transport u can drop.
Thanks for the info! I am staying in Gora.
My original itinerary starts with 9.27am Romancecar and estimate i'll finish the course at Moto Hakone around 4.30-5.00pm. It just that to travel back to Gora will take a while and some transfers in between. So lesser time to enjoy my ryokan haha