IMO this perspective comes only from the .... "Side quest isnt worth doing" perspective.

I would say that isnt a very good approach to a story based MMO game.
Its like saying you have to be paid to read a chapter of a story. I play for the game/storyline, rewards are only evaluated on a strategic basis. I often do not do sidequests, but that is because I often save them for later, when I need a quick burst of XP for a level, etc. And they are usually very easy when I have to go back to do a side quest. ;)

In reality they have taken great lengths to balance XP. They know many do not like to do side quests, so they have to make sure that the main quest line provides enough XP for a player to proceed through the game. Too much side quest XP, and pirates can be overpowered for the area they are currently questing.

Having played numerous characters I have noticed that there are various stages in the game where "more" xp being available would be a tremendous advantage (like trying to level before obtaining a new companion), but are very hard to find without venturing out of the areas your own pirate is limited to (by porting to friends). I have determined this is by design.

If they were to raise XP values for side quests it would require them to likely rebalance all quest rewards as well.

As much as I would love to get more XP for a side quest, I understand why they stand the way they are.
Perhaps adding/raising more nautical XP as a reward would help. Companion Training Tomes are an excellent reward, they get more and more valuable as a pirate proceeds.