Belton,
Don't worry, I didn't think you were criticizing. Interesting thoughts.
sanufi,
Katakana isn't bad itself. Katakana actually becomes a really useful way of representing things within a sentence, because it makes something stand out of a string of hiragana and kanji, and I can in fact recognize a familiar katakana word as quickly as I can familiar words written in kanji, hiragana, or English. It's only really troubling to read when entire passages are in katakana, as the speech of robots and foreigners are often written into, and also if I need to read unfamiliar katakana words quickly. But I still think most of the problem there still lies in relative unfamiliarity compared to the rest of the Japanese writing system.
The main problem is that they tend to overuse it, and since katakana loses it's transparency, it's kindof a pain (it's easy to us when the base language was English, but imagine how it must be for those who don't speak English. Most of them are like バイト - seemingly completely random). All languages loan, though. It's just more annoying here because they have more to lose, in my opinion. What's the big difference between "table" and "tsunami?" Nothing in particular. In contrast, what's the difference between テーブル and 津波? Exactly. I still like their use of katakana in general though. Adds spice. I just don't like how far they go with it sometimes. Reading a passage that contains more katakana words than kanji words makes something die inside.
As to kanji vs katakana in higher learning, it depends on the field. Computer sciences absolutely overflow with katakana, virtually all borrowed from English. More traditional (austere?) fields (medicine, law, whatever) are mostly kanji compounds for the concepts. I know I was worried earlier on that science words would be some mangled form of the Latin, as they are in most Western languages (you can compare a lot of scientific words in English and Russian and find they're exactly the same), but it turns out this isn't usually the case.
I want to stress, since you asked, that no matter how advanced the topic, kanji compounds don't really become complicated. You just never have to worry about words like 'stethoscope'. It's a 聴診器 - a listening device for medical examination (as the kanji imply). Heck, it's very similar to 盗聴器, a wiretap, which is a listening device for stealing(盗) what you listen to. Ramping up to stuff like 磁気共鳴画像法 can seem complicated, but no more so than actually saying 'magnetic resonance imaging' - usually less so, since the individual words are actually less complicated. And they tend to use the same acronyms we do. MRI. The only stuff that really gets me usually comes out of business and politics. For instance, I can't think of any particularly reason that 理事 should describe directors (or the boards thereof), especially not at first sight. But the words still aren't complicated, not like they are in English.
But, there is another valid complaint that's common to Japanese in general. While the Japanese words aren't complicated, they're all terribly similar. 聴診器 may be straightforward in meaning, but 聴診 is one of several words with the pronunciation ちょうしん, and let's not forget しょうしん、しょしん、ちょうし, etc. At least 'stethoscope' actually sounds unique - you're going to notice it when you hear it. Are you going to notice 聴診器 when it pops up in the middle of a sentence?
Katakana remains as it always is, for better or worse.