The majority of the "issues" (as have been discussed at length in previous threads) surround the fact that HM Religion, HM Magic, and HM Barbarians were written under HM2 rules, and were not updated when HM3 came out. There is an effort underway to publish an official HM3 errata. It should come as no surprise, however, that such efforts take some time to get through the CGI "process".
As for the clarity of specific rules/examples, that's obviously more of an issue for some folks than others, but on the whole, I don't think HM3 is a terribly complex game system.
No it's not a terrible complex game, personally I put it on the "Simple Games" shelf but that is because I spent most of my 90s playing HM1. Also during late 80s and perhaps also early 90s the complexity of the games grew (and with that the books needed to play them).
Perhaps HM3 is not Simple, more Medium, but when it comes to understand the rules, I have said it before, It is much easier for me that have played HM1 for so long. It is very important that the basics of the rulesystem is clean or is as clean as possible with (accurate) examples that helps new players to the game. HM3 is a very good rulebook, but then again, I have played HM1 so I have that back in my head when I read the rules.
I have myself players that are new (so they haven't played HM1) and they have asked questions, questions that I thought was obvious, but apparently obvious for me with 20 years of HM experience (and soon 30 years of RPG experience in general), less so for those that are new to the game and especially to those new to RPG.