I didn't like the runewords at all. They weren't easy to find out, without using some kind of internet guide. Who would like to expend all those runes trying to discover combinations. If runes were inter exchangeable in the slots, I would like them a little more. FF7 style.
I think the runeword system itself was a solid idea, just...wasn't implemented well. The fact that you weren't given a guide on how to set them up properly without looking up stuff online, or at least finding hints in the game that could point you in the right direction was one problem. The other big problem is that some runewords were just way, way, WAY too powerful...Enigma is the one that always comes to mind, and the fact that the higher level runes were (IMHO) a bit too rare for their own good. Not saying they should've dropped like candy, but shouldn't have been such a hassle to get. Though the fact that runes and SOJs and other things outstripped gold as a viable currency was a problem with gold and the lack of meaningful goldsinks and items to buy with it, but that's a whole 'nother can of worms.
One thing runewords DID do was that they gave more value to socketed items and those plain ol' white items you'd find. Finding that Archon Plate, or that Thresher you had been after for a while, saving up a socket quest from Larzuk, or taking a shot at socket rolling in the Cube and seeing you get the number of sockets you needed for the runes you had saved up...what a thrill that was! Will never forget how delighted I was to find a white Grand Matron Bow with +3 B&C Skills, rolling it in the cube, and shouting out when I saw 4 sockets pop up for my Faith Runeword. Yeah...runewords gave those 'common items' value, far beyond what they seem to have now in Diablo III and gave you something else to hunt after instead of just godly rares and Uniques.
It is a bit of a shame to see runewords aren't in Diablo III, and considering Blizzard has had A LOT of time to see and learn from the runewords of Diablo II, they could've made far more balanced ones. Of course, I know it won't happen now, but still...would've been nice all the same.