Gold and Silver did have a few new Water-types which were quite interesting and slightly marginal, and which as someone pointed out in the thread on 'forgotten Pokémon' elsewhere, are often quite obscure, as with Qwilfish and also Remoraid. While others like Dunsparce or Pineco did at least benefit from a fairly accessible or early location, as well as being known for things like the steel type or the Coil-Glare combination which makes them somewhat usable, these water Pokémon were often left behind, but at the same time their influx there in the fairly dark, closed in atmosphere of G/S was an interesting phenomenon. Part of the problem with them might be crowding, or that while the places they are usually found might be obscure and one might not look there specifically, they are very close to places like Olivine where a lot of events and such take place, or in general with a lot of white noise - and Jasmine has a domestic arrangement surrounded by a ring shape, which is weird and a bit problematic, given that they're not that old - and as such their location might come across as a bit too ambiguous to set them apart completely.
R/B were a bit more plain with Water-types, mostly relying on Water-types which were promoted quite heavily and well-known, like Lapras, Gyarados, etc. As such, Tentacruel can be annoying in G/S, but perhaps go along well with the emphasis there on less protruding Water-types. Of course, along with that, later Gyms do experience a certain crawl of Water-types, which might be a problem if you're not using Flying or such, which makes them oddly reliant on this for most of their main Pokémon. These are mostly earlier Pokémon, however, or R/B Water Pokémon, who might be emphasised in part to make up for G/S' own Water-types being slightly more on the obscure end. Still, though, while Feebas, which evolved into Milotic of course, was a bit gimmicky both in being found - and hence in a sense highlighted - and in its theme of evolution from the hidden Feebas to the 'pretty' Milotic along the lines of the ugly duckling, G/S seemed to get creating fairly obscure Water Pokémon about right, and they come across as 'realistic,' in a sense, or an organic part of the location and atmosphere, more than most others, rather than just a certain form which was promoted to you at a certain point and so on, like Shroomish or Ralts in R/S/E.
Different question, what cool underwater creature could they base a new Pokemon on that they haven't yet? A dolphin would look pretty awesome.
Since you mention type, a dolphin with a ghost second type could be pretty impressive, if done right. That said, they have gone in a cutesy direction of late, and a dolphin might be best avoiding this and retaining the slightly hidden and mysterious nature identified with the creature, or in brief appearing in a way slightly analogous to Mantine, rather than being forced to accommodate to such things or being presented straightforwardly. In general, a cutesy dolphin might just come across as a bit gimmicky, and in general a dolphin in the style of the R/B or G/S starters would seem more applicable.