Just to note the (possibly obvious) difference between whether to use a Travel Agent ... (the request of the OP) and simply organising a tour. While a TA can organise a tour, I think booking one yourself is easy and better. And this from one of the biggest fans of TAs on the forum!
Also, I an see the attraction of using a tour if you arrive on a cruise liner. Set and forget.
I think I'm not going to convince the OP, but in Moscow and St P, the thrill of discovering your own sights and experiences between the 'big name' attractions was a big plus for us. Being able to go to the roof of St Isaacs in St P wouldn't be on any tour, but was a highlight. Standing on Nevsky Prospect watching the passing parade of cars, hoons and humanity - fantastic (and we discovered the 'Soviet Cafe' where we had a memorable dinner!). The fountains in front of the Bolshoi in the evening ... getting up close to the guards in front of the Russian parliament and sharing a joke with them (

), finding a tasting room for Georgian wine, etc etc.
Take a tour .. book through a TA if you like. But save a day in each place for exploring by yourself. You'll love it.