The Brian Jones era is my favorite too, for the same reasons you mention. I feel their music had much more variety. Take 'Lady Jane', 'Have You Seen Your Mother Baby Standing in the Shadows', and 'We Love You', for examples.
Post-Brian Jones their music became locked into a particular 'Stonesy' formula (rootsy, swaggering, open G etc.). I have to say there's nothing wrong with having a formula either, if I listen to The Ramones, AC/DC, Chuck Berry or whoever I know what to expect, and I want it to be like that. The post-Jones Stones formula is a good one and some of their best songs were done to that formula. But I think I like the variety better.