education researcher here...
Few things to note:
1, Pisa scores are good in some manners but unreliable in others. Don't disregard them, but don't treat them as universal fact. E.g. years ago when they first introduced China to the PISA tables, it topped them massively. What followed was a clamor of politicians and companies trying to find out and copy how China manages their education programs.
In reality, the PISA trial with China only included select schools from Shanghai, China's richest city.. so in effect they were comparing entire diverse countries, to just the best students in the richest city of China, and funnily enough finding that those students do rather well.
So be a bit careful with PISA outcomes
2, Wales vs UK is a pointless comparison without regional breakdowns. in effect, in terms of size, population and distribution, Wales compares better to a region of the UK, rather than to the whole thing. I don't believe PISA scores differentiate between areas of the UK, but I would be entirely confident that what you will find is that London and the south east do much better than other regions, and that Wales is pretty comparable to the north of England in results.
3, However, with the disclaimers aside, could Wales just have poor educational policies? Absolutely. socio-economic factors do play a part, but only in conjunction with proper educational practices, and the reason for the difference is almost certainly a bit of both. However, to what extent is the Welsh government's fault, and to what extent it is the result of wider inequality - that would need much more focused research than PISA provides. I'm sure research on this already exists, if you want to find it.