Having actually studied this and written a paper on it in Uni, there are several bits to unpack re: potential enemies (which is utterly true for Classical Athens to be fair).

A: The "Athens" in the allegory is not Plato´s Athens, but "Mythic Athens". When I say Mythic, I don´t mean heroes and demigods running around messing with mortals. I mean an Athens in which any normal citizen would have held their own in an arm-wrestle with Hercules.

B: A theme running through that particular bit of Timaeus is "Utopia" or the perfect state. Mythic Athens was meant to be a shining example of that perfect state. Atlantis was meant to be a contrast to Utopia - a failed/failing city state which is falling from grace. (There is also a whole thread about Egypt and Athens as a modern contrast - Egypt as the Utopia state and Athens as an analogue for Atlantis - I digress, my professor was a big Egypt fan)

C: This meant that this "Mythic" or "Golden" Athens needed a suitably worthy foe who suffers a suitably fitting end. Athens represented all the worthy human virtues, while Atlantis was in moral depravity. Cue divine smiting - and when the gods smite, they smite hard. Why bring your current enemies into it and need to explain why they´re suddenly so much less impressive? Just make up a fictional city state and sink it when you´re done with it.

D: Using Thebes or Sparta also messes with the whole concept of "Athens used to be great, and now we´re shit and morally bankrupt". Pulls the message off focus.

E: The whole story of Atlantis in the allegory came from an Egyptian priest. Egypt had this whole mystique of "we redefine ancient wisdom" even back in 400-odd BC. Citing random "historical" (bear in mind the concept of history as a science and accurate portrayal of the past, rather than storytelling, would not come around seriously for another couple of centuries) facts as coming from an Egyptian priest is basically the ancient world equivalent of "trust me, I´m a scientist".

EDIT: Disclaimer - I wrote this paper about 10 years ago so memory might be hazy. It only really stuck in my memory because the professor was making a fun class a pain in the ass, and I wanted to ace the final coursework to prove a point.