I'd like to see more boat routes added for alliance, as well as a couple taken away.
Keep Existing:
* Menethil <> Theramore (Human ship)
* Feathermoon <> Feralas (Night Elven ship)
* Auberdine <> Rut'Theran (Night Elven ship)
Remove Existing:
* Auberdine <> SW (Human ship)
* Auberdine <> Alah'Thalas (Night Elven ship)
Add New:
* Menethil <> SW (Human ship)
* Menethil <> Alah'Thalas (High Elven ship)
* Menethil <> Southshore (Human ship)
* Auberdine <> Feathermoon (Night Elven ship)
* Auberdine <> Theramore (Human ship)
The advantages of this are several.
First is lore. The distance from SW to Alah'Thalas is only a fraction of the distance from Alah'Thalas to Auberdine - a journey of weeks, rather than months - and the humans and high elves have traditionally been allies even if relations have become strained recently. It just makes sense that the humans and dwarves would have been the first to sail to the high elves' aid, and would be the ones maintaining a constant supply route.
Second is gameplay flow. The current design feels like it pushes High Elf characters into levelling via Darkshore. My design puts them into Menethil Harbour after finishing their intro quests, making all three of the other levelling routes equidistant (more on that in a bit).
This also opens up travel that has traditionally been kind of annoying. Being able to get from the northern Night Elf stronghold to the southern one just makes sense, but it also makes it so alliance players don't have to run through either the Barrens or Desolace to get to southern Kalimdor.
As for SW <> Menethil and Menethil <> Southshore, this connects the eastern kingdoms maritime powers along trade routes they surely would have had in lore, and also makes it easier for players to get to these locations without needing to slog through Dun Morogh > Loch Modan > Wetlands or Wetlands > Arathi > Hillsbrad. The latter of those routes is particularly annoying, since at the level where Hillsbrad quests are appropriate, Arathi is almost a death run only saved by the fact that the there mobs are sparse.
Finally, this brings Menethil Harbour back to the central role it originally had. Players go to Menethil first, then from there they can easily get anywhere the Alliance holds sway. Auberdine is the centre of the Night Elves martine routes. Theramore is the centre of the human maritime routes on Kalimdor. Menethil is the centre of the Alliance maritime routes in the Eastern Kingdoms. And Stormwind once again has maritime access to the rest of the Alliance, instead of just the Night Elves.
To make this idea the best it could be, I'd also make two other relatively minor changes: I'd add a tunnel connecting Ironforge to Dun Agrath, so Dwarf players can access Menethil Habour without having to make a hero's voyage down to SW and back again or out to Loch Modan and back again, and I'd add a quest that Alliance characters can accept in Feathermoon Stronghold that flies them directly to Thalanaar, so accessing 1k Needles and Tanaris no longer involves any trekking through contested or high level territory.
Edit: If the issue of too many ships for too few docks is a problem in Menethil, the routes could be adjusted to go round robin or bouncing instead of direct - SW > Menethil > Theramore > Menethil > SW and Menethil > Southshore > Alah'Thalas > Menethil.
Edit #2: Depending on design philosophy, routes could also be added SW <> Booty Bay and Theramore <> Ratchet. Possibly Ratchet <> Steamwheedle Port?
TLDR:
* Auberdine goes to Rut'Theran, Feathermoon, and Theramore
* Theramore goes to Auberdine and Menethil
* Menethil goes to Theramore, Alah'Thalas, Southshore, and SW
* SW goes to Menethil only
* Alah'Thalas goes to Menethil only
* Feathermoon to Thalanaar is made easy mode with a free flight
* IF to Menethil is made easy mode with a walkable tunnel
* Feathermoon and Southshore are both made easy mode with new boat routes where none existed before