Plainly, if one were to sort out the overlaps, this ordering suggests the wonders found in the core British lists (1-14: See Arrangement) can be placed in "triads" - the traditional British form in which three similar articles were collected together, probably as pre-literate mnemonics (for a list of some of the extant Triads, see Bromwich* and Other Works). This seems particularly strong in the case of the last three mainland Welsh wonders (12;13;14), which are all tumuli (two of which change size).
No such triads are extant, however a weak indication that they may have existed, at least for some of the wonders, comes from Geoffrey of Monmouth's Historia Regum Britanniae (See Other Works). Geoffrey has Arthur quote the three lakes on their own (for no good reason) but with additional details not found in the Historia for Loch Lumonoy. This may suggest an independent triad. It is certainly true that the Severn is the only natural feature to have a triad in the extant versions ("The Three Defilements of the Severn"*). Very much more dubious is the dubious association of The Levitating Altar with Maen Cetti in Gower, and the even more dubious presence of Maen Cetti in the probably fraudulent triad "The Three Works of Might" (See Note).
This very weak evidence seems to be the only real support for the apparent triadic division by theme. Stylistically, for example, one could organise the wonders thus:
Short
vs. long
vs. connected with stories about people
Equally, the latter could be divided by saints
vs. Arthur
Or one could divide some by stuff tested
vs. Stuff that kills you if you test it