well, from what I have heard here on line, people have been taking a wide range of options as to where to set the various parts of AoW in Eberron, so this is only my personal answer. Keith Baker's conversion notes put Alhaster in the Lhazar Principalities on the NE end of Khorvaire, specifically between Skairn and Tantamar - making it a pivotal but not major princedom (also presumably because the Lhazaarites value seafaring most and Zeech isn't the seacaptain type). This is fine with me in general, but I don't like the location between Skairn and Tantamar. I decided to place Alhaster farther east and south, specifically south of Cliffscrape, north of Q'barra, and east/northeast of the Boneyard. The advantages to this being several:
1) It's on the edge of the Lhazaar territory so Zeech's peculiarities seem to fit in better
2) It's a port between Q'Barra and Lhazaar so that emphasizes A;haster's role as a trading port and haven for nefarious types from both regions
3) Taking Baker's placement of the Rift Canyon as being Goradra Gap in Eberron's Mror Holds, this allows a quick airship run from Alhaster to Goradra along the Ironroot Mountains without passing over any inhabited area (going from the location between Skairn and Tantamar you need to pass over/thru the most populated areas of the Mror Holds
4) It lets me put the city of Saltmarsh (from DMGII) on the Q'Barra coast along the Basura Swamp peninsula that faces Tempest Isle, setting up a nice little area of trade and further adventures
5 and relating most to your question) This leaves the PC's controlling and independent kingdom between Lhazaar and Q'Barra with Talenta & Mror just over the mountains, linking Cliffscrape to Slatmarsh and other Q'Barran ports. As epic level characters they may take on the Dragon hiding in the Q'Barran ruins, or seek to become Dread Pirates and terrorize or rule the Lhazaar Princapalities, while also facing growing influence from the Inspired in Q'Barra and the threat of Erandis d'Vol from the north.
Anyway - that's my take on it
For me that doesn't directly change the politics of Eberron. The most major effect is that there are these powerful heroes in the eastern fringe not under anyone's direct influence, but beset on all sides by potential opposition. The PCs couls unify the eastern coasts as a force against Riedra or just be legendary trouble makers out east without really changing the politics of the 5 nations, so it can still go in any direction.