Shugenja aren’t just jacks of all trades, they’re (or at least can be) pretty much masters of most. Bushi or courtiers are nowhere near as versatile and depending on what it is they specialize in, often barely or not better at whatever it is they do best. An iaijutsu duelist should be better at such duels than a shugenja and a courtier should be better at negotiations, but tanking damage, dealing damage and investigation are things a shugenja is better at than anyone else (yes, a shugenja is typically a better investigator than a Kitsuki). The number of spell slots is the only thing that keeps them in check, but I rarely see that actually come into play in published adventures and it’s something that’s hard to enforce on the fly. Medicine checks notwithstanding (which are restricted to once/day per patient and need a not-insignificant investment in skill ranks to be effective) shugenja are also the only source of healing. Iaijutsu duels and negotiations tend to be challenges that are difficult to put in adventures with meaningful consequences for failure too, but difficult is not impossible at least.
If they were D&D wizards they might actually be easier to handle. I completely agree about the playstyle thing, absolutely, but mechanically speaking their spells being prayers means they can use any spell they know as often as their Rings allow without preparation, with Void slots as wildcards. Using Spellcraft to learn more prayers is fairly easy, 4th is all about the low rank spells so reliability is rarely an issue, and particularly Commune (which can be used with a slot from any element too) is far too good. A D&D wizard at least has to prepare spells, Vancian magic style. Being pacifistic is a restriction, but that’s a choice - looking at my Tamori here.
If I make the antagonist a capable magic user, it becomes really hard for a party without shugenja to counter the machinations of the adventure. A little illusion here, some spell-fueled superhuman actions there and a party without magic ends up chasing shadows until I just reveal what’s been going on and they can try to make some sort of heroic last stand (which is terrible adventure building). I can only attest to personal experience, but every GM I know reworks their adventure when they find out the party won’t have a shugenja. And again, that’s not an issue exclusive to 4th. Every edition has this to an extent. But my impression is 3rd has it less.
To me this discussion just shows we all have our preferences and priorities. For you having to scrap a school (or a technique at any rate, I doubt there are many schools that have more than 2 busted techs) is a fundamental flaw, for me that’s one of the easiest problems to solve because it’s an isolated mechanical issue. For me every edition is playable as is (disregarding the d20 version for a sec since it’s not R&K and that makes it irrelevant for me, that’s a completely different game), including 2nd which I largely skipped because I really disliked that iteration of the R&K mechanic. I’ll play 1st again in a heartbeat. I actually play 4th most basically because it’s the current edition and current is what most people want to play. I have no fundamental objections against any edition, and as far as I can tell now that will go for 5th as well. 3rd is just the one that for me is the most engaging with the least amount of adjustments.