I should preface this by saying most of my chargen work assumes Missions, which means that the level of opposition is relatively flat. If you're 100+ karma into a progressively harder campaign, different rules apply.
Agility isn't worth it because there there aren't really situations in which you'd need to be one above your augmented maximum. A lightly-cybered (eqv.) shooter can get to 18 dice very easily, which hits 9 vs. 9 defense dice at an acceptable rate (I consider 85% success acceptable when I'm building characters). An optimized shooter (Agi 6(+4), Skill 6, Specialization +2, Smartgun System +2, Reflex Recorder +1) shoots with 21 dice. At this point, you're already risking wasting hits with most guns, so adding an additional die isn't going to give you much.
Edge isn't a bad choice, but I don't think it's good enough to be considered a default choice. Low Edge characters have problems, but once you get to an Edge of 4-6, you generally have enough (unless your GM is really harsh about refreshing it). Combat in Shadowrun is short--if I'm rolling initiative for a third time in a single combat, I automatically start to get worried. If I've build a reasonably competent character, I'll only fail 15% of the time, so maybe I'll use one Edge per combat to offset a bad roll. Another Edge for "dramatic success," another to save me by adding to a defense test, and another to not get feared, and I've only spent 5. For me to get to the point that I'd need the 8th Edge point with a human character, I'd have to be playing in marathon sessions with loads of different combats or in very small groups in which every character was expected to have multiple specialties, thereby increasing the number of "critical" rolls (and roles) each character performs. My Edge 5 Missions character is about 150 karma into things and he's run out of Edge exactly once. Edge is universally useful, but an infinite supply of it isn't needed. The resources needed to make a character Lucky could probably be better spent making that character competent, eliminating the need for him to be Lucky.
Resonance wins because it's the most universally helpful attribute in the game and it's used in tests that are difficult to augment. It beats out Magic because Magic isn't rolled for Drain and magicians have other means available to them (spirits, foci) to add dice to their tests and it's easier to tailor your character around the specializations of Spellcasting than it is the specializations of Resonance-linked skills. Magic is still very good, but certain types of magicians don't really need it. You can have a functional mid-magic character; you can't really have a functional mid-resonance character.
Intuition comes in a distant third because it's hard to boost to its augmented maximum without dedicated mage help and it has universally helpful applications. Perception is one of those "must have" skills, but really, it's here because it adds to your defense tests. As anyone who has tried to shoot a PhysAd with 16+ defense dice can tell you, defense tests matter. Adding one die to a test in which you (generally) win ties can swing things tremendously, especially when you're facing heavier ordnance that's difficult to soak even conceding one net hit.
