No specific tools, but addressing a few points you and others raise:
Provide a text-only option. It's backwards-compatible, and while the old-timer argument carries weight (console mail client support), many mobile devices offer what's little better than a console-equivalent email experience.
If you generate links, make them short. I'd recommend fewer than 40 characters, fewer than 20 if you can. They travel far better.
Email isn't the Web. Clients differ, and ultimately HTML is not universally supported. You're relying on an opt-in preference, which is to say, you're relying on a self-selected community which will progressively reinforce your initial biases toward content presentation regardless of its validity. Beware that.
My favourite illustration of this is the "Six o'clock on Tuesdays Club meeting time prefernce question". If you ask a group of people in a club meeting at 6:00 pm on Tuesdays what time they prefer to meet -- it will strongly tend to be "6:00 pm on Tuesday", as you've already self-selected for those who prefer and can accomodate that option.
Email clients are inconsistent. Web clients are inconsistent. Fucking text editors are inconsistent (character support, font support, kerning, foreground / background colors, ...). Basically: fucking deal with it.
I'd avoid use of inline CSS entirely -- the less explicit layout you perform the better and more future-proof you are. Limit formatting to bold and italics _only_, and realize that _that_ may not get conveyed reliably. Numeric and bulleted lists should be explicit, not HTML entities. Basically: pre-render absolutely everything if possible. Don't use tables for layout, I'd be leery about them even for tabular data presentation.
Especially: avoid use of contrasting text colors to convey meaning, they're frequently stripped from generated output, e.g., by Mobile email clients.
Graphs: include images. For now, PNG is preferred (best rendering of line graphics), though modestly compressed JPG will occupy less space. Keep an eye on SVG support though. It's an _excellent_ format for rendering data visualization (though you'll absolutely want to down-sample large datasets), and there are libraries which support graphics creation. Client support is still developing, but should be widespread within a few years. All current major desktop clients provide decent support. Legacy browsers and other HTML-enabled tools, not so much.
Email / Web UI duplication: as above for email, that's a fact of life. Fucking deal with it.
Though I generally dislike PDFs, if you're preparing reports to be delivered to users, dropping a PDF or link to same is probably your best bet. Many browsers will now present these natively, many mobile devices (though not all) have some level of PDF support.
If you do this, I strongly recommend:
1. Use generator tools which create the smallest possible PDF possible. Many bloat output to a staggering degree. Bandwidth, mailbox size limitations, and other factors all favor _small_ attachments, still.
2. Landscape layouts. That's generally preferable for desktop viewing. While mobile devices are frequently presented portrait, it's far easier to perform a 90° transform on a Smartphone or tablet than a laptop or desktop monitor.
3. Put the executive summary and highlights in the email itself, detail in the reports.
There are a few alternative forms of delivery you might consider, among them RSS, and ePub or other eBook formats (far more flexible presentation, especialy on mobile). My read is that these aren't universally acceptable, but choosing a tool or tools which supports these and offering the option(s) to users might help clarify your future direction.