Phonetic input system works like crap for a language like Mandarin, and most Sinitic languages, where you have to choose a Hanji from sometimes hundreds of homophones.
When choosing Hanji on a computer system with a phonetic system, it requires you to take you eyes off your input area, and divert your attention to the little box from your IME. It constantly breaks your train of thought and is actually bad for your eyes. It is even worse for your wrist if you end up selecting a Hanji with your mouse.
Boshiamy, Cangjie or any other IME that breaks Hanji into parts is extremely useful if you do academic stuff. Phonetic IMEs’ auto select are trained with daily usage, which completely breaks down when you want to enter technical terms or do higher level Chinese homework.
I personally use Boshiamy, and I chose to do so because even though I could get 70 characters per minute out of New Zhuyin on Windows in a ideal condition (no Hanji selection required), it just gets in the way.
When I decided to do so after researching for the best option, I disabled my New Zhuyin and just went for it. It was tough at first, but it only took 2 weeks before I felt I could type most of the stuff without needing to look it up.
With Boshiamy, I get at least 100 characters per minute, and instead of selecting 2 or 3 characters every sentence, I would at most select a character every paragraph.
If you choose one of the Cangjie derived IMEs, I would suggest try out 大新倉頡. It’s basically Cangjie with Boshiamy style rule. So you would at most enter 4 alphabets per character.
Of course, that only works if your learned to write Hanji before you learned how to type. If you can only speak the language, then Pinyin or Zhuyin would be the sane choice.
If you do use Zhuyin, I would suggest switch the Zhuyin keyboard layout to the Hsu layout (許氏鍵盤).