I'd like to describe a workflow using this option mentioned by user568458: 
> - **Code up a web-based chart in something like D3, then extract the SVG** output from a web browser, then open this in Illustrator and finish it for print there. The New York Times do this sometimes, [I discussed this and how to get exact CMYK colours in this other question](http://graphicdesign.stackexchange.com/questions/18714/is-there-anything-that-can-read-import-or-convert-cmyk-svg).

I have given up on Illustrator's bronze age tool for doing charts of poll answers (mostly bar/column graphs, pie charts and line plots). Illustrator couldn't handle corrections, small tweaks or updated data - any modification ruined the layout. I also couldn't specify key dimensions that had to stay constant throughout the set of charts (bar height, font size, max height).

Check out [JSGraphs.com](http://www.jsgraphs.com/), tons of JavaScript graphing frameworks are compared there, and you can pick the most suitable one for your project.

I also used [python livereload](https://pypi.python.org/pypi/livereload) to live code (auto-refresh on save, actually). It gets things moving along faster! Navigate to the project folder in command prompt / terminal and just type `livereload`. All project files are now served and can be accessed on URLs like `http://localhost:35729/chart-01.html`.

It takes an up-front investment of time to learn the charting framework, its quirks and limitations, but once your first few charts are built you can use them as templates, sometimes just plugging in new data, changing nothing else.

My framework would accept CSV files as input, which I got by exporting from .xlsx files. Plugging in new data was done by changing one line of code `url: 'resources/graph-02.csv'`

Color themes could also be managed similarly with a JSON file.

From here on up to delivering CMYK EPSes much of the workflow can be automated.

Depending on the framework, exporting to SVG can be as easy as <kbd>Ctrl</kbd><kbd>S</kbd>. If it's embedded in the HTML markup as an SVG element you can batch export it with Playfair.

[justinmanley/playfair: Generate charts and graphs from the command line using d3 and PhantomJS.](https://github.com/justinmanley/playfair). 

Initially I just used UI automation tools that would replicate enter-URL-save-as-enter-next-URL-save-as monkey-work for each file in the folder - AutoHotkey or [WASP for PowerShell](http://wasp.codeplex.com).

To batch convert SVGs to CMYK EPS files I made an [action in Illustrator.](/questions/67006/how-to-batch-convert-rgb-to-cmyk-and-have-black-mapped-to-0c-0m-0y-100k)