I was on Remora 2004~2010 until the server was merged with Leviathan. Admittedly server numbers were higher then, the game was different etc. But even so the server merge made no difference to me as a player really, I still did my fishing and Pup stuff on the new server and it didn't really affect me. Obviously we all felt sad to see Remora die, and have nostalgia for it etc. but that is all it is - just nostalgia. In practical terms that server merge didn't spoil the game for me or anyone I know.
Also I've been stuck on the final Seekers battle for a while, none of my friends or fellow LS members do Seekers missions, and it seems that people who wanted that win did it in the week after update (when I was snowed under with work!!!) and are too busy to join shout for it now. So server merge would help with things like that, more people doing missions or having the mission-clear KI so they can enter the fight again, makes mission fights easier to group up in.
I don't mind at all if they merge servers, tbh I'm happy with w/e they do that keeps the game online and retaining its basic FFXI essence as much as possible. I have a lot of admiration for SE for many of the positive changes they have made to the game in the past year or so, and for soldiering on to keep the game fun after all this time. If they want to merge servers I won't say anything either way, they do what is best for their product and hopefully the customers too.