There are a number of systemic problems that should be fixed if there is a 5E. And these are things I think are problems. There are other things I'm not a fan of (like super-lethality or some schools being so good at something that anyone else trying is basically useless) that have some arguable purpose and are to greater or lesser extent a matter of opinion. But there are things like:
- shugenja are crazily overpowered
- grappling has some issues (unless I'm mixing this up with 3E)
- weapons are not balanced (and in a way other than "the katana is best," because there would be an arguable thematic justification for that)
- the transition to getting two attacks a round (in general I think they should smooth out the gains from schools, but you definitely don't want this big of a power hump for bushi ... despite the fact that it's the biggest thing that a bushi might get and yet they're still much weaker than shugenja)
- most characters (aka, bushi) have all of their crunch focused around combat mechanics, but the combat mechanics for the game are vague and wildly open to exploits
There is no thematic reason for these that I am aware of. With regards to #5, I understand that there is a design purpose to having vague combat mechanics, and having vague combat mechanics is fine ... so long as they don't appear in a game with characters centered almost entirely around combat and require players/GMs to just ignore some character options/tactics because they destroy the game. And I get that some people think these things are a big deal, and some people think these things are not a big deal. But if they aren't providing anything positive to the game, it doesn't really matter if there a Big Deal or not - if you're making a new version of the game, there's no reason not to fix them.