Hi -- this is a good general question but it is also a rather difficult high-level question, and one might need quite a bit of experience in real musicological work to be able to answer.
While Sonic Visualiser and the available plugins provide some tools for breaking down music in interpretable ways, it is still very hard to work backwards from a recording to details of things like instrumental balance or local dynamic or tempo variation in a classical work, not least because most methods are primarily designed for pop/rock music. (Even local tempo estimation and "beat tracking" are essentially unsolved problems for classical music.)
One thing that is quite valuable is to load multiple recordings into Sonic Visualiser and then time-align them -- for this you need the MATCH plugin installed. This can give you some information about the conductor's decisions in terms of both overall and local tempo. There is a video showing this at http://sonicvisualiser.org/videos.html#2
(Audio alignment using Sonic Visualiser and MATCH).
The videos from Musicology for the Masses may also be of interest, as well as "A musicologist's guide to Sonic Visualiser" (http://www.charm.rhul.ac.uk/analysing/p9_1.html
), but (as you have probably seen already) these primarily focus on Sonic Visualiser's built-in visualisation tools rather than higher-level analysis using Vamp plugins.
It's quite possible you may get interesting results from plugins that analyse tonality (possibly even the "Key Strength Plot" from the very basic key estimator in the QM Vamp Plugins set) or loudness (there are various options for analysing amplitude -- we have a proper auditory-model loudness plugin in the works but it isn't quite published yet).