There are a few men that can do it all (Hanyu, Javi, etc.)
The biggest calling card for Javi and Hanyu has been their gorgeous suspended-in-the-air quads when they are in the zone. They've had some great programs that they have grown into over the years for sure, and their quad expertise racked up so many points and rep during their tenure at the top, which allowed them the opportunity to remain at the top while improving some of their weaknesses. They are both compelling in many respects when they are on, which is largely due to their competitiveness under the coaching expertise of Brian Orser. And yet, IMHO, they have been consistently over-scored on PCS, effectively told for years they have nothing to work on in most PCS categories, which is not true. However, because it seems to be true based on scoring results that certainly provides them with a significant advantage in being practically unbeatable (unless they totally flop with more than two or three errors).
Frankly it's the huge point values for quads that has separated them from the rest of the field.
The truth is that they each have some weaknesses artistically that are completely shrugged off. They are both okay in terms of presentation generally, but IMO, Javi has lacked range and neither Hanyu nor Javi are the greatest ever interpreters of music and choreography. They have both managed to find their niche and comfort zone however and to work sometimes brilliantly within what they are capable of doing. I think Javi has grown more in terms of interpretive ability, but again within a certain niche that works for him. Hanyu can stand to improve his stretch and posture. And fortunately for Hanyu, Orser helped him solve his nagging lack of endurance problem late in free programs. Neither Javi nor Hanyu possess the musical understanding and expressive movement qualities of Jason Brown, Adam Rippon and Jeremy Abbott -- even Nathan Chen has a better understanding of musical nuance than Javi and Hanyu, though Nathan still has room to grow in terms of maturity and refinement.
Both Javi and Hanyu have experienced consistent patches of inconsistencies, which have generally been excused by 'how hard it is to land boffo quads, so we should just give them a break.'

They have certainly received a boat load of breaks on PCS points and tech points over the years. In addition, there's no doubt that both are extremely popular in the skating community and among fans, with powerful federations backing them up. (The one-two punch of Japan and Canada -- despite Javi coming from a smaller fed, he's clearly helped by his charming likeability and by training in Canada with the right coach who helped him improve all aspects of his skating).
I would have to include Patrick Chan, Denis Ten, Dai Takahashi, and Tatsuki Machida as being a notch above Hanyu and Javi when speaking of complete skaters who have won major medals (excepting for the beauty of Hanyu's and Javi's quads when they are in the zone and not popping or falling). Patrick, Denis, Hanyu and Javi have all suffered from competitive inconsistencies, but again it's been usually shrugged off as being due to having to focus on quads. Of the four, Denis took awhile to master quads and to improve his level, and in recent years he began to falter due to injuries, apparent lack of focus and other issues.
Despite Patrick Chan not having fully mastered more than two basic quads, he's better than everyone on the basis of his skating skills, and the purposeful intention he has shown in his focus on improving artistically. At his best, sans the current quad factor, Patrick has had flashes of being unbeatable. However, with the quad factor in the mix, it's become more difficult for Patrick to sustain dominance in his comeback. And sadly, post-2011, it was Patrick's over-rewarded inconsistencies that began the 'falls are okay as long as you make the 4 revolutions,' lame justification for over-rewarding certain skaters for revolving with botched landings.
The sport or the people running it don't seem to have a solid clue exactly where to land on the quad issue. It was okay apparently when Javi and Hanyu were leading the pack with flawed, consistently over-scored performances, mixed with sometimes brilliant performances. But with the new young guns rising and flashing an expanded repertoire of quads, somehow that has placed a spotlight on the problematic disparities of overdone point values for quads that in fact always existed since the changes were first instituted post-2010 Olympics.