The gun remains above the sand, so why doesn't he use it while submerged(or is that supposed to be a parascope)? My thought is that he'd come out of the sand to recharge with solar panels or something... In addition, you could have him submerge completely, and use A_MoveAbsolute to have him re-emerge elsewhere on the battlefield.
Now, for some more practical concerns. Because you use sprites instead of actual horizontal movement to submerge and emerge from the sand, once eggman emerges from the sand, his sprite is not representative of his hitbox... that is, you only hit him if you aim where the top of the eggmobile would be if he were submerged.
Otherwise this is a fine boss. Its very nice to see something new. Also, the boss music kinda sucks.