I hear your pain, traveller. I'm currently building the Admiral Kuznetsov (a gift from a most wonderful wife) alongside the 1/200th Sovremenny and I can say that as much as I admire Trumpeter for going full throttle with intriguing subjects in big scales, they do have a bit of refining to do in how they "engineer" the kits. Fit issues do abound (probably inevitable with some BIG parts, although I did have a surprisingly easy time with the Kuznetsov top and bottom hull), but my biggest frustration is with the small parts. A lot of them are attached to the sprue in weird places where runner is stronger than the parts themselves. The instructions do leave a bit to be desired as well.
Trumpeter is a relative newcomer and they have put a lot of product out in a short time, so I guess alot of their quirks will dissipate as they refine their processes. We take the experiences of Hasegawa/Tamiya for granted, but they've been in the industry for decades. On the other hand, Accurate Miniatures puts out some great planes, but it takes them years to come out with anything new.
I guess my best recommendation is to maintain patient perserverence. The end result will definitely be impressive.