So, this is something I come up with while doing my dishes. Everything is about to be proposed here is still very premature and all inputs and critics are welcome.
For TL;DL, skip 'Premise' and straight to the 'Deconstructing WvW' and 'Introducing Mega-Server' section.
The game mode has been long plagued with two major issues related to the server-based matchmaking system and the score system.
First of all, it is indeed technically impossible to balance population and time zone difference among different servers. Speaking from a player's perspective, we hardly log in and just get an equal match, and when we do, it slips away the next match comes up, if not just next weekend for some major guild decides to black out, or even just next hour due to off time and prime time.
Next, the score system simply does not reflect the effort players and guild/communities commits. You maybe having a great time and some successful result tonight, sure. But then, the next evening you log in and find your server scoring the third, and all objectives you spent time to hold and tier up yesterday lost, simply due to lack of coverage by and organization of players from different time zone during your daytime.
The developers aim to tackle these issues with the upcoming restructuring. We will be distributed into different 'Worlds' no longer based on the server we are in. Instead, a new system, Alliance, will become the new standard. 
Now, I am not going into every single detail about the new system. In case anyone is still new or out of loop, please refer to the link above. What I intend to propose here is that, the new system still kinda misses the point. You see, we will still be getting 'Seasonal Matches', some fixed, non-dynamic distribution of the playerbase for an extensive period of time (based on the info at hand, 8 weeks, or a 'Season'). But, say, what if during the span some guild just for any reason decides to take a time off or restructure or simply dissolve? What if a new episode of living story comes up and some players just get diverted?
Equal matches will never be created for an extensive period of time like this, and a World-based score system will never truly reflect the effort individual guilds/communities and players put in. To put a score on a real-time world persisting through 24-7 is way too demanding for the community overall, and overestimating the organizational power of the latter. The only server we've ever seen to have been consistently achieving such is Blackgate, and none.
No more fixed 'World'. No more Seasons. No more expectation of cross-timezone organization. No more obligatory participation throughout the match and the stress comes with it. No more non sense score system that does not reflect the performance of you and your community.
What the playerbase of the game mode need is something different, something real-time. A match-making system that is based on the population at the moment, and distribute the players accordingly for the moment.
What is fundamental to this game mode? Not for scores. Not for material rewards.
People play WvW to fight, together with other people, against other people. This is what constitutes the core of the experience. The entire game mode is centered around communities, however the size of which may be.
We need a system built around it. The Alliance system proposed by the developers is a good step forward to the right direction, but we need an even more radical approach. Matchups should be consistently more or less equal at any given moment, and scores should reflect the performance of the guilds/communities so that they can finally become meaningful.
A system that does not create 'World', that is, a fixed distribution of the playerbase over an extensive period of time, but rather, a system that creates matches based on more or less real-time population.
A system without a global, 'World-wide' scoreboard, but scoreboard for individual players and guilds.
How may this be achieved? We already have the tool at hand: the Mega-Server system. A system that creates maps according to the real-time population at hand.
Instead of 'Worlds' and 'Seasons' that last over weeks and 24-7, we will be getting far shorter match-ups -- each lasting for only 2 or 3 hours max with a new map generated for its duration. A guild may 'Sign Up' for a match within 10 minutes before the match starts with a roaster of participating members, and the system will create matches accordingly, similar to how the developers currently plan. Several similar sized guilds will be pitched against each other, in addition to individual roamers and party-sized groups, which may participate without signing and just hot-join to be automatically distributed to a random match.
During the 2 or 3 hour match, a score system will record the performance of you as individual, as well as your guild, and put a score/rating and perhaps even game-mode specific rewards accordingly. Say, guilds may earn special rewards for completing objectives in a match. Heck, maybe even new guild missions to provide goals and step up the competition!
Plus, only a necessary amount of maps will be created at any given moment, so the chance of dead, empty maps should be minimized, and ArenaNet can power off some of its servers during off-time to save the planet. (and perhaps their electricity bill :P)
This way, we get far better match-ups, far better experience, far more true score system to your performance, far better community building. This is the WvW as players want it to be.
(Some tweaking will certainly have to be implemented though, such as lower amount of delivery per tier required to tier up an objective and such, new, smaller maps for matches during off-time, guild-based-only squad system in the game mode. But those will be easy to solve.)