Organized tours, no doubt have their own advantages, and I have taken such tours earlier, specially when travelling within India (I find it safer in fact, rather than travelling in public transport carting my clan of girls). They usually cover up all the touristy places, which I of course love. What is travelling, if one is not going to go see the iconic monuments of a place. Imagine going to Paris and not seeing the Eiffel tower, or going to Agra and skipping on the Taj Mahal.
At the same time, the tour bus may cover up places you would rather skip, take you to shopping areas when you don’t want to shop. Added to the tight time bound schedule (searching for the loo just as it is time to get back on the bus) and getting mixed up on the hordes of tourist buses lined up that look more or less the same (and the tour guide always threatening to leave without you for not being on time back or all the rest being delayed because an unapologetic honeymoon couple decided to take their own time clicking photos of each other like it is their last).
I would rather make our own self-guided tour of places we want to see and get on the public transport at our own pace and time and freedom to detour if we want to. Walking is the single best way to take in the sights. The bus is always the preferred mode as one can see more of a place rather than the underground metro or tube. If one researches well enough there are local buses that do take on some very touristy routes at a fraction of a cost. Besides the people tend to be more helpful on the bus than the hurried working crowd on the train. Travelling in a bus, specially in Europe is a no brainer.
However, if you do get a good bargain on the Hop on Hop off (HOHO) buses, it is worth it as they have family fares. You get a route map, commentary (free headphones), open bus top with an option of sitting below and indoors if need be and yet be at your own pace. Paris and Dubai are such large cities, but we were able to cover the length and breath of it with the HOHO, which otherwise would have been impossible on bus and foot.