I'm a long-time GM of RuneQuest and long-time DM of D&D. I'm Cross-posting from ENWorld:
I own MRQ, Glorantha books, Lankhmar... you name it. I even wrote
an ENWorld review of MRQ. I'll get Elric of Melniboné RPG and Hawkmoon RPG ASAP (and own the previous editions, as well as a whole bunch of Glorantha third age material, herowars... and so on). Just to provide the context.
First, I think MRQ as a system should be differentiated from Glorantha, the setting (the ducks, broos and so on). It's like saying "Forgotten Realms" for D&D, if you see what I mean.
Then, as far as the systems' comparison go, these are IMO two systems built for different uses in mind. Where D&D strives to be precise in terms, rules and sub-rules, RuneQuest provides general guidelines you are free to build on and adjudicate as you want. It also provides a different type of Fantasy: D&D is great for campaigns with characters who have steady mechanical advantages piling up as they go; with RuneQuest, everything has basically two/three types of scales - normal heroes and legendary heroes (with the experienced hero, with Skills around 80%, in between).
RuneQuest is easy to customize. It's easy to use. The rules aren't long to read. The characters can be created real quick.
As I put it somewhere else:
MRQ is more rules-light and more adaptive than DnD on some levels. See, DnD provides a precise type of fantasy and entertainment. It has its levels, its classes and prestige classes, and a whole host of rules and sub-rules to play with. It's cool sometimes to have that level of detail and customization, and this precision in the elements of game balance and design. When you are considering like I do that the rules may support the immersion and vivid feeling of a fantasy world (and thus aren't opposites), this can be a great help.
Sometimes, however, you want to be able to just roll some dice and get the game moving. You will not want to spend a lot of time on the tactical aspects of the game. You will want to be able to take the rulebook and say "ah, geez, frack this!" and roll with your instinct to adjudicate situations and just well, go on playing the game. Sometimes even, you'll search for a rules frame, as opposed to a complete interdependent game system, that just allows you to customize and build rules on the go, to make the system your own.
MRQ does all this stuff really well, for me.
There's also a difference in the types of fictions MRQ and DnD simulate. Playing people who feel more like the "average joe" and try to survive in a world that is just as large, if not larger, than themselves will fit more MRQ's intent by the way it is framed with the use of percentages and roll-under mechanics.
If however I want to have characters starting very low to achieve extreme power gradually while still retaining the fun of struggles and dice rolling on a large scale of character development and concentrating on contrasts within the character from start to finish, the discrepancies between levels and the open-ended mechanic of "roll+bonus vs. difficulty" which can scale on and on forever, will probably be more appropriate.
Hope this helps. BP.