To answer some of the basic points (that haven't already been covered
), Gene Roddenberry was only responsible one specific "rule" which is that there couldn't be an odd number of nacelles. They had to be even to make a balanced warp field, and he seemed to think that having one nacelle was like building a helicopter with only one big rotor, and without the means to counter the rotor's torque so it could fly. Since he wasn't an actual engineer and we've seen designs that either break this rule or ignore other elements, I just ignore it myself. Andrew Probert came up with the rule about nacelles ideally having LoS between them, as with the warbird.
Its funny, most of my favorite ship designs (the canon Niagra class and Freedom class, and the FJ destroyer [Saladin class]) have odd number nacelles. While the rule kind of makes sense, the fact that it seems to have been done more to screw with FJ than to make the universe better/more realistic makes me glad that TNG and later ignored the rule.
As for the BoP, I've never had a problem with there being different sizes. I've always thought it made sense, using a proven design but modifying it for different roles (in this case, increasing the size, probably to make it tougher in a fight). It would have been cool to see different ships than the BoP all the time, but having a bunch of mass produced ships makes sense for a warrior race like the klingons. Producing the same design a lot is easier and faster to build than having a lot of different types of ships.