But they made the Loop basically the same value as the Flip, and they did the same to the Salchow and the Toe-Loop.
That's because those pairs of jumps have long been considered almost interchangeable in difficulty. In fact, it's very common for skaters (intermediate to junior level, whenever they're ready) to start learning the triple salchow before attempting triple toe -- it's just that once they do learn the two jumps the toe loop tends to be more consistent, and also easier to include in combinations.
As for loop and flip, again, it tends to be a matter of preference whether the skater is an edge jumper or a toe jumper. There are probably almost as many skaters who can do triple flip but not loop as the other way around. It may be that (on average -- everyone is different) men tend to prefer the flip and women the loop. But unless there are going to be completely separate scales of values for each sex, there's no good argument for valuing the flip much higher than the loop. Certainly the original point values in which the triple loop value was equidistant between that of the triple salchow and triple flip was most out of whack -- triple loop is much closer in difficulty to triple flip.
I, too, thought that gee if the top women can land fully rotated 3-3's, then the next evolution should be quads, right?
Well, that's one way of looking at it, but it's a pretty superficial approach. Adding more revolutions is obvious but for most women, given the current state of training techniques, equipment, Earth gravity, and human anatomy, women rotating 4 times in the air is not going to be possible.
I'd think a breakthrough in skate technology that facilitates higher jumps with appropriate support on the landings would be the most likely factor to change to make quads more feasible for human women.
So meanwhile, what are the other areas where today's real-life skaters could push the technical boundaries?
Correct takeoff technique and full rotation on all triples have already been mentioned in this thread.
Jump combinations. Triple-triple combinations are becoming less rare. As long as three-jump combinations are legal in the long program, triple-triple-triple is something to aspire to that no woman has yet done in competition and hardly any men.
Triple something-triple loop is still rare. Maybe for good reason, given all the injuries such combinations led to 10-15 years ago, Tara Lipinski being the poster child for both the loop combos and the hip injuries. Also rotating the loops enough to avoid downgrades or underrotation calls is much more difficult than with other triple-triples.
Triple something-half loop-triple flip is another option I don't think we've seen in competition from any women.
Double something landed on the other foot - triple salchow (or flip) would be another place to add difficulty. If the rules gave bonuses to second jumps in combination, that would be incentive for skaters to develop that skill.
Ditto with jumps in both directions, or double walleys and inside axels, eventually in combination.
Combinations of jumps with other skills. Already there is room in the scoring system for judges to reward jumps with difficult entries (or exits) both in the GOE and in the Transitions component, although these rewards are less codified than the base marks for harder elements. Still, if a skater gets to the point where she can land all the triples (up to lutz if not axel) with good technique, ease, and consistency, and difficult combinations, but cannot add more rotations, then weaving the triples into difficult steps as well would be another area in which to add difficulty.
None of which would be easy to codify or to tout to non-fans who don't pay attention to anything but number of rotations and what TV commentators tell them are the more difficult takeoffs. Still, people within the sport as well as interested fans can appreciate difficult combinations of jumps and difficult connections between jumps and other skills, and rules could be changed to better reward things that are so difficult that they're not worth trying without better mechanisms to reward them.
, she cant even land a clean Lutz 
