Beamer is an excellent package by Till Tantau for using latex to create slides. It can be used to create effective presentations and slides. As an example of a very good use of beamer, Karl Broman shows how to create handouts with notes.
Although I agree that you can make good academic talks with beamer, it takes a lot of experience and effort. This is because the skills required to give good talks are largely different from the skills required to write good papers. Beamer (latex) has so many features that allure you to make ineffective presentations. Thus, I strongly encourage starting students to refrain from using beamer until they learn how to give effective talks.
Beamer (latex) makes it way too easy to put equations on your slides. You lose half your audience every time you use an equation (by Stephen Hawking). You should avoid putting equations in talks as much as possible. However, beamer makes it too convenient to put equations on your slides.
It seems that many are tempted to reuse materials (such as equations and algorithms) from the paper, since it was also written in latex. Moreover, even the structure of the talk may mimic that of the paper. Make sure you make a fresh start when making slides.
Even figures and tables should be re-designed. You rarely want to show the exact same figure from the paper in the talk. In the paper, you want to be comprehensive. In the talk, you want to extract the necessary information to convey your point.
The default font size is way too small. I use 28pt (in PowerPoint) for the top-level text, and I still think it may be too small. The default font size of latex corresponds to somewhere around 20pt in the same scale.
Having such a small font size makes it very easy to create slides full of text that are never effective. Of course it is simple to change the font size in latex, but fresh students tend to use the default.
Another possible latex effect, in combination with the small font size, is the use of full sentences. Since you are in latex world, it is easy to write sentences, even paragraphs. You only need to put key phrases in your slides, but some settles with sentences, since it fits your slide with the default font size.
Apparently (before my time, in contrast to the use of transparent), PowerPoint was criticized for encouraging boring talks that are sequence of bullet point slides. Beamer does no better than PowerPoint in this regard. Many beamer presentations I have seen were essentially entirely made with itemize/enumerate.
I don't think bullet points are bad. You may want to mostly avoid them for exceptional occasions, but for regular academic talks, bullet point slides without too much text work fine. It becomes problematic when there is nothing but bullets.
Tools like PowerPoint have features to create simple drawings with basic shapes and lines. You just have to move some objects around with your mouse to visualize key concepts. This is not possible with beamer. You can of course import figures in latex, so this is not a limitation of beamer. However, beamer can discourage you to use figures, since you need to make the figures in some external tools or via some packages (just like when writing papers).
My goal is not to say that you shouldn't use beamer to make your slides. The bad practices mentioned in this page is not at all specific to beamer. However, I hope that you agree that beamer can encourage these bad practices, especially excessive use of equations. I emphasize that I only discourage inexperienced students to use beamer.
Once you have learned how to make your talk effective, which tool you use is simply your preference. I have used beamer a number of times myself. I eventually decided that it is easier to make the slides that I want with PowerPoint for academic talks, but it may be different for others.