Deep Dark Galaxy; A Hybrid Level of Jolly Roger Bay and Dire Dire Docks?
With it's creepy atmosphere, and a few nicked elements from earlier in the game, it wouldn't really surprise anyone that the level design of Deep Dark Galaxy includes a lot of similarities to the past water levels from Super Mario 64.
For one thing, it is the closest level in atmosphere to the Super Mario 64/DS levels underwater, because it is a level which is NOT set among the sunshine lit landscape with palm trees, clear blue skies and crystal seas. It has a darker feeling very much more similar to the gloomy and dull locales that are Jolly Roger Bay and Dire Dire Docks, where the former had a 'forgotten pirate cove' feel of mystery and the latter had a more gritty, industrial settings filled with dangerous hazards and sea life. But that's only a minor thing that is shared compared to the other similarities.
First off, compare it to Dire Dire Docks. If you enter in the third mission and go down, there is a huge amount of sea life in the underground lake which is a relatively creepy atmosphere. This seems almost parallel to the first area in Dire Dire Docks which had multiple sharks, cheep cheeps, a manta ray and other dangerous aquatic creatures lurking around while this version instead has more gringrills (eels), bloopers and jellyfish (with the odd cheep cheep near the bottom and various deep sea but harmless fish). I really did feel like the same setting was here when I tried to get the third star (Guppy in the Underground Lake) because of this.
Another but more obvious thing is that of Guppy and the ring challenge. You have to swim through 8 rings and the rings slightly refill your air, which is similar to the Manta Ray challenge from Super Mario 64 where you have to swim through the rings and it's your life that is slightly refilled by going through each ring. Both of these things are for stars, and both are very late in the level mission order.
Landscape is also comparable, as is general level design. Dire Dire Docks had one deep lake with multiple forms of sea life and things lurking around at the bottom for bonuses and then a tunnel which led to a second watery area with more of a mechanical feel, less creatures and some exploration above the surface. Deep Dark Galaxy seems to have the same, with the first sea life infested lake going deep under the surface, a tunnel and then a second area where certain stars have you explore the shore. Heck, the ship is even there in the same way Bowser's Submarine was in the Dire Dire Docks level. Plus, these things have to boarded for the first star in the level.
I can also say it is similar in other things. The deserted beach with shells, treasure chests on the sea floor and various power ups to collect to progress. All that and at least one level in each where you must explore the higher areas of part of the level (the pole jumping in the Nintendo game game, the cliff exploration in Galaxy). It also feels so familiar in the design and exploration.
Now to look at Jolly Roger Bay. The first you'll notice is the similar wording in mission titles as shown by these two examples:
'Plunder in the Sunken Ship'
'Plunder the Purple Coins'
Both are pretty similar uses of wording, yet one is from Super Mario 64 (DS) and one is from Super Mario Galaxy. This seems rather inspired (and Nintendo seem to like the word plunder a lot in reference to water levels).
And then there are the ships themselves. Sure, the graphics don't exactly look similar because of graphical constraints and different graphic styles, but the premise is still there. First mission in both is based right around the ships, referring to them even in the mission titles. The coin collecting is then heavily based around collecting coins ON the ships, with the red coins in the original and purple coins in Super Mario Galaxy. Heck, you could even count the obvious pirate style of the ships in each level.
Jolly Roger Bay also has an underwater cavern. It also has a bit of necessary cliff exploration for red coins and stars.
For another point, there is a common theme of the level with it's music being foreboding and almost eerily calm in these levels. The other quiet music in the background, the more scary type music as you explore the murky depths. It's all there. Even the level name, with the common type of alliteration in the titles. Dire Dire Docks. Deep Dark Galaxy.
In conclusion though, it does feel like Deep Dark Galaxy is a kind of spiritual successor to the forementioned water levels, and also like Nintendo intended it to be that way, in bleak contrast to over happiness found in Beach Bowl and Sea Slide, and shared in the Drip Drop and possibly Bigmouth galaxies. Did they intend it? I think so, but I guess it's up to the invidual player to decide for themself.