The great thing about Japan is that it doesn't matter what time of the year you're going, there's always something different to see and do. You can also vary which part of Japan you go to, so that the weather suits you better. For example if you want to see the sakura but can't catch it in time in Kanto, you can head north instead, where it blooms slightly later.
The same applies to Hokkaido. Each season offers different things to see and do, even if you've been there once you might want to go back there again during a different season.
One main consideration of independent travel however, is how to get around Hokkaido. Train services in Hokkaido like the rest of Japan, are highly efficient, punctual and a very convenient way of getting around. If you're sticking to just a few places such as Sapporo, Hakodate, Noboribetsu or a ski resort, you might want to consider just getting the rail pass and sticking to the trains.
If you're interested in heading further north and east to the national parks though, you might want to consider driving. Access to these areas is difficult without a car, and most of the time, it takes just as long by train as it does by car. Driving offers much more flexibility, the beautiful scenic routes are an attraction in themselves, and you can make stops at the attractions along the way. Car rental is pretty painless with companies like Toyota present in almost every city. They entertain last minute changes and one-way drop offs, and you can just pick up the phone and call them for bookings.
A GPS system is installed in almost every car, and although its only in Japanese, the "mapcode" system whereby you just key in the code of the location you are going to makes it easy for non-Japanese speakers. Alternatively, you can also key in your destination by the phone number. English driving maps are abundant, and most including this one come with the scenic drives and relevant mapcodes nicely planned for you. GPS directions are very detailed with nice big arrows and things like traffic lights, junctions and lanes, and even facilities like convenience stores and banks clearly marked out.
Just 2 things to note. Firstly, you need to get an International Driving Permit (painless procedure in Singapore). Secondly, Hokkaido is obviously subject to really low temperatures, and I haven't experienced driving there in snow conditions. As most of the roads in the national parks have wide lanes and are really well-maintained (even the second-tier roads), I don't foresee that this would be a problem with good tyres and snow chains.
Driving trips are really fun because you never know what wonders you might stumble across on the way, such as random fields of potato flowers or sunny yellow flowers.
