I rode there ten years ago now, it was great. I picked a fairly flat route as I didn't set off till September and I was chasing the winter, and I broadly followed the rivers. From Zeebrugge, Antwerp, canals to Maastricht, over to the Rhine, Main, Tauber, Altmuhl and Danube until Serbia. The official Danube cycle route was basically off-road after Bratislava, though it may have improved since.
Apart from a few hills in Germany, it was fairly flat until Serbia. The east got a bit hillier but it was fantastic, limestone valleys that reminded me of home. I got lost in Fruska Gora national park, which was brilliant.
Depends what you want to see and do - the Tauber valley is a popular cycling route (there are two options, Der Klassiker and the hilly one), and it's peppered with hilltop villages that are exactly how you imagine Bavaria to be. Beer festivals, cuckoo clocks, oompah bands etc.
Oh, I took a shortcut across Hungary to skip a meander in the Danube, and someone said I missed one of the best bits as it went through a narrow gorge.
Can't really comment on lodgings, I was mainly wild camping and finding cheap hostels in the cities. The cities are great, I probably should have visited the Tesla Museum while I was on Belgrade, and Plovdiv was a great place, you can feel the centuries beating down upon you.
All a bit vague, I know, but one specific bit of advice is not to ride into Istanbul along the main E80 route coming in from Edirne, it is a mad multi lane carriageway with traffic coming at you from all sides. Among my adventures was nearly getting sideswiped by a BMW (the driver heard me swear at him, stopped in the middle of the road, waved me over, said "Peace!" and offered a fistbump), then getting carried away filtering past cars on a downhill stretch, failing to spot a lump of concrete stuck to the road, and getting some Good Air. Which is not such a good thing on a heavily-loaded tourer. I did have mental images of the frame snapping under me before I landed. Mind you, reaching the Roman wall at dusk was a glorious moment, especially cos they led me down to an actual cyclepath along the Marmaris to Sultanahmet.
Presumably you'll have a GPS rather than a map of Turkey at 1:1 000000 scale