I agree completely with Anaris: no matter how you go about it, any major change like those proposed here will result in complaints, loss of players (hopefully short term) and accusations of preferential treatment.
I also think Indirik presents a reasonable approach: If such major changes are desired/needed/accepted, it might be better to start from scratch. Instead of changing existing islands or merging them, create a new one, have others migrate to it, then close the old ones. If a combined world is desired, just create one new world-island and have all characters migrate to it, then close all islands.
I also see Constantine's point: The layout of a map probably has a huge influence in how things play out and what war opportunities there may be. On the flip side, if players discover geographically advantageous positions, why are they not fighting like mad for possession? Are these positions so advantageous that there is no hope at all?
Also, even if we started changing geography in an attempt to "even the playing field", it is nearly guaranteed that different geographically advantageous positions will be found. Then we would have to change things again and they cycle would repeat. Now, however, players are constantly frustrated because their city just turned into a rural region and that damn mountain keeps moving. I still believe that, though some geography might lend itself to combat more than others, it is ultimately up to the players to make pick fights and make things fun.