Putting together an effective presentation and visual aid (i.e. slide deck) is very time consuming, very iterative, requires a lot of thought and reflection, at least a few reviewers that are removed from putting it together and/or the topic, and a lot of practice. Reducing presentation to simply putting together a slide deck is a fail from the get-go. Blaming bad presentations on the tools used to put them together is shallow.
While there is really no substitute for good coaching, first hand experience, mistakes made and good feedback, here are a few quick tips that I've picked up over the years -
1. The best and most engaging presentations simply have a title that captures the key point and a nice/fun background photo that supports/illustrates the story. Audience will pay attention to the story instead of reading text off the slide.
2. To highlight a fact, keep it to one fact per slide. Make it short and direct (e.g. "3x faster" rather than "212.32% performance improvement").
3. To illustrate a quantitative point, one chart per page is okay, but it must be super simple and easy (absolutely no 3D nonsense, at most 3-4 bars/2 lines/3-4 pie slices, clearly labeled axes). Multiple charts are sometimes okay, but they must be each super simple, belong together, have the same scales and tell a clear and obvious story. Effective charts are a topic of its own, anything by Tufte is a great head start.
4. If you must have more than one point on a slide, keep it at 3 direct, concise bullets per page (if any bullet wraps with a large font, it's too wordy and unclear). No sub-bullets or additional explanations should be necessary. Two bullets is too little (i.e. condense it to one key point), four is too much.
5. No more than one simple diagram per page. Best to keep it to the title that captures they key point and a diagram. Additional explanatory text should not be necessary - if title + diagram can't stand on their own, they are not good enough. Also, if the point of the diagram is not immediately obvious to someone looking at it for the first time, the diagram sucks.
6. Avoid wall of text (e.g. that NASA slide on Columbia's tiles) at all costs. Audience will start reading the slide, completely tune out what you are saying and then get bored half a way through and give up.
7. Contrasting points or showing contradictory data/ideas requires extra care to avoid cognitive dissonance.
8. Background should be as plain as possible. White is best, black/gray could be okay. Anything else pretty much sucks. All text in one color, with great contrast to the background.
9. Timing/length of presentation is super important. Generally, it is very hard for people to stay focused for more than ~7 minutes, so it's good to cover a point in less than 7 minutes and then change it up a bit (e.g. change presenters, show a video, get to a different topic). Overall, presentations should be less than 30 minutes, 45 minutes tops. Anything longer than that is simply too long, you'll lose the audience.
Here are two books on the topic I found helpful. They are easy to follow, very short and to the point - "Style: Toward Clarity and Grace" [1] and "Guide to Managerial Communication" [2].
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Overall, the piece feels quite trashy - it dumps all the blame where it doesn't belong (tool vs. lack of presentation/communication skill). Those slides could have very well been made in Keynote or Reveal.JS and they wouldn't suck any less. The piece is also not constructive, it doesn't give reader any hints or tips how to make presentations better.
Finally, a great counterexample to the main point of the piece is pretty much every slide deck that comes with Apple/Steve Jobs' keynote. The best part is that no one remembers or pays particular attention to the deck, but if you analyze the presentation more closely or watch it a couple of times, it becomes clear how effective the decks are.
[1] http://www.amazon.com/gp/product/0226899152
[2] http://www.amazon.com/gp/product/013297133X