Its up to you bro. But I'd strongly recommend F&E if you really want to experience Hokkaido like it was meant to be. As well as to have a glimpse of how Hokkaido pple live everyday.
Join tour groups if you like to be herald ard and let others tell you where to go and what to do. And to restrict yourself to those few touristy attractions only.
And don't forget, you still need to pay tour guide fee at the end of your trip. And if you suay suay encountered a lazy guide (like I did back in 2008) that brings u to shopping and more shopping for the entire trip, you will feel damn TL paying for that sum of $$
FYI, its typically NOT TRUE that F&E will cost more than packaged tours. This is esp true if you're going with your family of 3 or 4.
Tour groups earned big profits from the way they charge for the tour. They charge everything by per pax. For F&E, you pay for per hotel room price for your family.. cos you guys will be staying together. And if your room rates includes half board (breakfast n dinner), your whole family gets to have a full meal, be it buffet or more excusite set meals.
That applies to rental cars as well. You guys all travel in a car, and the rental is charged per car for x number of days.
of cos la, all local tour agencies will go out of biz if everyone plan our tours like many of us here do. But its an inevitable trend that will pick up pace quickly as the use of internet expands.
For me, I search the net for best deals and then book from either the source (eg JAL tickets) or through dedicated online tour wholesellers eg hotel.com and booking.com . The same applies to car rental as well.
And then I search the net for info on the attractions that I'm planning to go.
You may also make a trip to JNTO office at Hong Leong Building 15th floor to collect some Hokkaido travel related brochures and info. If you plan early and happens to come across some Hokkaido fair org by Hokkaido tourism board, you will have access to even more detailed info on the towns and cities you wish to go. Things eg driving maps will be available then.
Itt may take a little big of effort on your side, but its well worth it and you'd have a sense of satisfaction when you see your hardwork unfold in front of you when you start the trip