@"Ronin.4501" You're seeing "Alliances" as "replacement Servers" and that's not the case. Alliances is actually about guilds as a base unit for WvW.
I agree that some players would try to stack in a good guild (so they can be part of a successful alliance) however players themselves control guild membership in a way that doesn't happen with servers.
If the Alliances WvW update ever comes to be, Anet will use guilds and alliances of guilds to make the population for each side in WvW. This is a much more flexible system because guilds vary so much in size and this granularity will allow Anet to create more even population sizes for match-ups. This is something that has been seen as a major need in WvW for years.
I foresee many more complaints about "elite" guilds requiring specific builds, or kicking players who are inactive or incompetent.
There will likely be some large open or pug guilds, and some dedicated guilds (probably smaller). In theory each existing server could make a Guild with that name and continue the situation as it is, but I doubt this will happen. There will still be the drama of guilds leaving alliances and going elsewhere, so in that sense there will be more of the same. BUT the big difference is that we as players will have a lot more control over who is in each Guild/Alliance. Anet will still set the links between alliances and guilds, and this is where it is important the system used works properly.
For example, a secondary benefit of Alliances, if Anet get the algorithms right, is the matching system could pit fight based alliances against other similar guilds/alliances so these players will get more of the play style they enjoy, and similarly match PPT guilds against other PPT guilds. Small guilds and single players will fill the gaps. The stats to do this are already available to Anet.
In theory, Alliances (which is really Guilds vs Guilds) should give us more enjoyable matches and more even overall populations. This IS a thing worth hoping for (we've been asking for this for years). Of course, in reality, it actually needs to happen to be of benefit to players, and as you say it needs to be balanced separately from PvE (although there are signs that Anet is possibly moving to make this work?).
GW2 is the game I've spent the most time playing, and I still enjoy playing. I'd like to continue to enjoy WvW, so you'll have to forgive me if I, and others, choose to hope against all expectation and current evidence.