Pros and Cons of Base Types

Surface Castle
Your average base nothing special, probably a large wall and maybe even a tower with a large keep in the center to keep all of your loot.

Pros:

• Easily accessible to members and other allys
• Testament to strength
• Intimidation
• Surveillance

Cons:

• Easy to find
• Able to tnt cannon a hole in the side
• Hard to defend
• Players can Ender Pearl in
• Resource/labor intensive

Underground
Any sort of structure of tunnels and chambers made underground, might even be a converted stronghold or mine shaft. These are a extremely safe bet if your worried about being found.


Pros:

• Hard to find 
• Small hallways for traps
• Quick access to ores
• Hard if not impossible to tnt cannon in

Cons:

• Lonely 
• Farms take a long time to set up
• Boring
• Getting to the surface can be a hassle
• No early warning system for raids

Underwater
Usually a portal into a under ground base but can also be a bio-sphere of sorts.


Pros:

• Extremely hard to locate 
• If set up correctly enemies will drown when they try to enter
• Fast access to surface 
• Infinite fish
• Iron grip on the ink sac market

Cons:

• Friendly's might drown
• Very obvious where your base is at night if their is a light glowing
• Might forget where the entrance is and drown
• Roof leaks

Battle Tower
My personal favorite, the battle tower is a 16x16 chunk that is preferably claimed with factions and constructed with obsidian.

Pros:

• Impenetrable 
• Peace of mind
• Partially underground and/or underwater
• Great early warning capabilities

Cons:

• Extremely obvious where your base is especially when its covered with lava
• Very cramped (If you have a large clan you can build a second tower so the whole thing is 32x16)