Hi there
I own both Mongoose editions of Runequest (and a few of the older ones), and I was quite disappointed by the first edition and very pleased by the second.
In my opinion, a number of serious improvements have been made, substantially more than that between 3.0 and 3.5 D&D. The attack resolution mechanic is entirely different, for one thing! Combat is fluid and easy to resolve, and beating an enemy's defense gives you options to perform manoeuvres which make combat much more cinematic.
The spells and magic have also received a number of strong differences as well, generally, made more powerful than in first edition. Character creation is also quite different; characters will be able to be more realised than in the first edition.
In every part of the game, I saw particular bug bears of mine from the first edition (having to possess physical runes, the lack of depth to starting characters, the clunky combat mechanics) removed, and replaced with smoother mechanics. In a number of places (notable the combat manoeuvre system), innovative and fun mechanics also shine through.
I would highly recommend the new edition of the game; the proviso is that some of the early supplemental releases are not showing the same polish and care that went into the main book. Mongoose seem to be aware of this and even (I may be reading this into some of their responses) a little ashamed of it, so I hope that they improve going forward.