There is probably a difference between deviating from the methods of the Rishonim on intrinsic Torah issues, and deviating from them as a result of extra-Judaic developments. For example, the Rishonim were bothered by certain questions that bothered the philosphers of their day, and weren't bothered by others that the contemporary philosophers didn't care about (or never thought of). Moderns find some of the great medieval philosophic questions to be unimportant or trivially answerable, and have other problems that bother them which the Rishonim never dealt with. These shifts in what bothers people are often attributable not to deteriorating Torah knowledge and instincts, but to changes in how external society thinks. The Rishonim were influenced by the thought of external society just as we are, and the questions they pondered and answers they wrote because of that influence are not necessarily any more valid than the questions and answers our generation is inspired to offer by the equivalent influence in our times.
(Comment originally posted at http://hirhurim.blogspot.com/2007/03/musings-on-proper-way-to-learn-chumash.html.)