I did the Europe Uncovered tour 2 years ago and fully recommend it.
As for your questions, the hotels were all decent enough from memory. You don’t need them to be too grand because you don’t spend any time there aside from sleeping and maybe an hour to shower/freshen up before you go out in the evening. The only bad one that sticks out was Paris. Bad in that the room was extremely small and the 2 beds were so close it was almost like sleeping in a double bed with someone you’ve only just met that day, and the bathroom was pretty cramped and in need of renovating. Also the lift could only fit 1 person with luggage so it took a while to get everyone to their rooms when we arrived. But from what I heard from the Topdeck staff, every tour uses a different hotel in Paris so hardly ever the same one twice and they are pretty much all like that there.
Don’t remember anything disappointing from any others though. Mt Rigi sticks out as being spectacular. Massive room, nice new looking bathroom, great bar downstairs with pool table and views of the Swiss Alps out your window to wake up to. But it would have to be good because you can’t exactly go out anywhere else for the evening once you’re up the mountain! Few of us played a bit of football on a patch of grass up there and got quite tired and puffed out very quickly - the air up a Swiss mountain is quite a lot thinner and I’m used to in New Zealand!
Couple of places didn’t have air conditioning so it was a bit warm overnight and a couple also didnt have lifts, but then you only had to walk up 1 or 2 floors anyway. Hotels were generally in good locations and good enough for the amount of time you’re going to spend in them. Where an included meal was at a hotel they weren’t always particularly good though. The meal in Rome was awful - I was given the vegetarian option due to the meal being pork which I can’t have and it was just a slab of cheese and some peas. Our tour leader made a big complaint about it.
As for bus times, generally we would leave first thing in the morning (8ish from memory) and get to the destination sometime in the early afternoon/evening. Journies can be long or short depending on where we were going. Paris to Rigi was the longest and due to roadworks and traffic etc we only just made it to Rigi in time to catch the last train up the mounting (ie, our tour leader sprinting off our bus to stop the train leaving). But some journies were also quite shortBut they do a good job of keeping it interesting as we got a few movies on the bus and played some games etc. It’s also a good opportunity to catch up on a bit of sleep if you have a very late night or I also used the time to write a diary of my trip while the previous day or 2 were still fresh in my mind. You get regular stops every couple of hours too.
Generally when you have 2 nights in a city you would arrive there late in the day, then have the whole day the next day.
Happy to answer any questions about the tour or specific locations.