Transcribe with /j/ or /y/?

I’m teaching phonology again, and once again, I am contemplating the issue of which phonetic system to use. It seems like a trivial issue, but it actually gets into some tricky issues.
One of the trickier issues is transcribing the “y” sound of “yes”.

FROM Y TO J

Although linguists generally stick to IPA, there is a close variant called American Transcription. Usually, I just teach both (and accept both for credit), but I do like to stick to one variant in my lecture notes if at all possible.
The “y” sound is /y/ in American, but /j/ in IPA (following German spelling convention). In the past, I used /y/ in order not to confuse my students who are generally familiar with English/French/Spanish – all of which spell this sound as “y”.
Americanyes = /yɛs/ boy = /boy/
IPA – yes = /jɛs/ boy = /boj/
This time I have changed my mind and have moved to /j/. One reason is that all other Penn State classes use IPA. Another is that even the Wikipedia uses /j/. At this point, I’m starting to look a little “backwards” for sticking with American /y/ instead of the more continental /j/.

NOT A COMPLETE SWITCH

But I haven’t made a complete switch…Following Kentowicz’s 1994 textbook Generative Phonology, I still prefer American for some sounds. Some because they show phonological relations more clearly (per Kenstowicz). Others because, quite frankly, it’s easier to crank them out on a keyboard.
Some examples
* I use American /ñ/ (as in señor) instead of IPA /ɲ/ for the palatal nasal.
This is because a) it’s easy to type /ñ/ (especially on a Mac), b) American students are familiar with the Spanish sound and c) there are too many n’s with tails in IPA (ŋ ɲ ɳ). At small point sizes, I think it’s easier to spot ñ.
* I use American /ṭ,ḍ,ṇ/ instead of IPA /ʈ,ɖ,ɳ/ for retroflexes.
This one is because a) almost all scholars of language of India (the prime retroflex languages) use the dot underneath b) I can generate these on the Mac extended keyboard and c) I still don’t like that IPA retroflex tail visually.
* I use American /ü,ö/ instead of IPA /y,ø/ for front rounded vowels.
Because 1) German spelling uses umlauts and b) it signals “front rounded”. It also means I never have to use /y/ in transcriptions – avoiding the whole “What does /y/ mean?” issue.
* I use American /č,ǰ/ instead of IPA /tʃ,dʒ/ for alveolo-palatal affricates
The reason for this one is that even affricates are supposed to be “two sounds”, they are generally treated as a special kind of stop in most languages. Interestingly Indic scripts all treat these two sounds as one letter, as does Arabic (and English “j” and Italian “c”).
Just to be weird though, I use IPA /ʃ,ʒ/ instead of /š,ž/. This was clearer to many students for some reason, and they are distinct in shape. These IPA symbols are also very common in French linguistics.
I won’t claim that this is a perfect solution – after all IPA is becoming more of a universal standard these days than when I was learning linguistics. If nothing else though, I do like to mention the alternates because both were in use for a long time.
A linguist (even me) has to learn to make adjustments for different linguistic documents.

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