I have just returned from an organised spotting trip to Russia and I have to say that it IS the way to go about doing the hobby in Russia without hassle. Permissions were granted in advance plus a knowledgable translator on board our coach made things easy. Also hotels are very very expensive so sharing rooms is cheaper.
Before this trip I did think about doing it by myself, but I am glad I didn't .......I can now see that it would have been difficult and I would have seen/photographed far less.
I organised a small group to go round Moscow in the Spring of 2006 with official permissions (all for a large amount of dollars) etc and we were stopped by the militia/security at all four main airports in Moscow.
Even at Bykovo our visit was terminated right at the beginning because of concerns over the Russian presidential Tu-204s there, despite the fact they had no engines and had been there for a couple of years.
Our translator had to pay a lot of dollars to get us out of Vnukovo...
Apart from Bykovo we had no problems during the official visits themselves, it was when the official tour was over (or when people went back) then the problems started.
I think the most money changed hands in getting us into Myatchkovo (as my mates hadn't been there before). They know the value of entry these days.