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I think in some cases, it can be a fair criticism, in my honest opinion (although it's too much of a generalization because occasionally engineering classes will cover a topic more intuitively and therefore with better insight than some formal math course or something). My first semester of electromagnetism was my favorite EE class because it was more conceptual. However, with the second semester, everyone else thought it was much easier, but I found it in poor taste and basically stopped following the class and tried to teach myself the subject on my own, with not so good results. I ended up dropping the class and the major. The more cookbook approach may have been great for everyone else, but I was punished for wanting to understand. I struggled, not because of genuine difficulty, but because it just wasn't my style, and I didn't want to compromise my way of learning. If you think I'm making excuses here, does it make sense that everyone else thought the first semester was the harder class?
This sort of thing is more common in engineering classes than in physics or math, but most of them aren't so bad. In most of my EE classes, I was able to learn with understanding pretty well. There were just a few of the classes that really got on my nerves that way. It causes us the more conceptual thinkers real suffering when are forced to sit through these ordeals. The fact is that it doesn't need to be taught that way. It's not the subject's fault. However, if you try to do it in what I think is the right way, most of the students will be upset, and it will be the few conceptual ones who are happy, and so that's the unfortunate situation in some of the engineering classes. In the less deep subjects where everything is more straight-forward, this isn't so much of an issue.
Of course, math and physics are not immune from this sort of thing, either, despite their facade of being "deeper". In my experience, mathematicians seem to be quite fond of pulling definitions and concepts from out of the blue with no motivation--and quite needlessly, too, in many cases. To me, that's the worst kind of cookbook teaching, just as bad or worse than what you'll come across in engineering. But overall, math is probably the place where people are the most conceptual in their thinking, at least in undergraduate classes. So, the reality is that someone who is more conceptual would probably be happiest as a math major, in all fairness. However, it still might not be the right choice because eventually, they are going to have to get a job, and maybe engineering would suit them better than being a math professor. I think applies to me. I actually liked the better part of EE, but I just had a particularly strong distaste for a few of the classes that I took, and was really intrigued by math, so I went for that, but it was probably a mistake in the long run. In hindsight, I think I should have just done a double major in math and EE and left it at that. My grades in engineering were a mixed bag, but in math, I had close to a 4.0 after I changed my major to it, so at the time, it seemed like it was a better choice because it seemed much more natural to me. I think it may be because I am very error-prone in calculations (as opposed to proofs), plus dealing with bad textbooks (textbook quality seems to go down as you go on in most fields) for the first time and that sort of thing. Another reason I think I did well in math was that when I studied EE, it taught me a lot about how to learn. I think if I went back to EE now, I'd do much better (I wasn't a bad EE student, by the way, just not as good as math). It's not even controversial that math major math is "harder" than engineering math. Most of the engineers will admit it, assuming they are in a position to judge.
Another thing to mention is that doing proof-based math is very different from engineering math, and some people will have a strong preference for one or the other. Unfortunately, the proof-based stuff has more limited practical use (you can do engineering math in a more proof-based style, but the particular subject matter studied by mathematicians these days is mostly not too practical).