About the Magic system, I haven't actually used it, only read the rules and the spell descriptions, so my view may be off a bit (or a lot). However, like I said, there may be some minor issues when using them in a more generic (aka. D&D style environment).
Firstly, in Glorantha there is the assumption that everybody can use certain type of spells depending on which cult you belong to, I guess. I know the rulebook actually mentions that this may not be desirable in certain other settings, but nevertheless the assumption affect the magic rules, and also brings the cults more to the fore. Not necessarily a problem, but may turn off some people.
This is related to the concept of common magic, and the other more specialised types. How do you use common magic in environments where magic casting ability is reserved only for mages/priests etc? Do you simply make up cults which use certain types, and then limit 'non-casters' status in these cults as laymen, etc? Are common spells just 'petty magic' or 'cantrips' compared with the more specialised Sorcery and Divine magic? Common magic certainly doesn't seem very common or low level, there are some quite powerful spells there, it seems? And what to do about Sprit Magic, does it actually have a place in certain settings? I can see where exorcism and spirit combat might have it's place (like priests casting out devils in Deus Vult or something)?
Of course, lot of this depends on your setting but I can see where the RQII RAW may cause some dilemmas to solve, especially if you're not a RQ veteran. It certainly has cause me to pause and try to figure this out. It's not so much the rules themselves, but the organisation of the system of cults/spells so they fit in your setting. I actually like the rules very much, how devine magic works, and how flexible and powerful sorcery seems etc.
Which reminds me of one other possible concern, the potential for development a caster has. Unlike games like D&D, where the potential is almost limitless, in RQII the potential is limited to POW and magic points which, if I am not mistaken, are not easy to rise, or at least not insanely so, than in D&D. The improvement seems more subtle and smaller in scale. You get better skills for the most part. For a player weaned on D&D etc. it might seem rather insignificant, even? Of course, it's the same for combat as well. No levels, no insane bonuses, extra attacks (unless you pay insane development points) etc. Everything is more compact and subtle. I am not saying this is bad thing, quite the opposite. But it might be a turnoff for some people?
One another thing about magic that might be problematic in a more generic setting is enchanted items (ie. Magic items) as described in Arms & Equipment. I seem to remember that you need to dedicate either POW or magic points to crete them? So this would seem a big sacrifice for the magic user, and how do you explain this mechanism in a setting, when +1 swords and rings of protection are common as mud? Have there have been hordes of magic item creating mages in times past, and they didn't mind handing these out like free candy, or what? Again, the mechanism is rather nice and subtle, and reminds me of the One Ring type of deal in LOTR, where Sauron poured a lot of his power into the ring (magic points), and now wants it back. Magic items seem therefore much more personal and important for their creators. Very nice, but how does it fit to a setting where magic items seem to be overly common?
It would be interesting to hear what you more experienced RQ GMs think of these issues? Or are they in fact issues at all? I am in the process of trying to convert the system into a setting using some D&D 3.x material, so this would be especially helpful for me.
Oh, and another thing: Mongoose, when you make Wayfarer, please make a GM screen that's actually useful!?