When graphing large sets of data, plotting fewer points but still representing the data visually can be challenging. Loading 500 vs. 5000 points can help improve load time and reduce system resources. A co-worker pointed me in the direction of a downsampling plugin for flot charts. The author, Svein Steinarsson, published a paper detailing several downlsampling algorithms for graphs.
If you're looking to get some accurate graphs with decrease in load time, I'd recommend using the Largest-Triangle-Three Bucket method. It provides accurate results quickly.