To understand this simply learn the spelling rules for Welsh then sing along with the first line of the second verse of the Welsh national anthem, known in English as 'Land of our fathers':

"Hen Gymru fynyddig, paradwys y bardd"

("Old mountainous Wales, the bard's paradise".) In other words, Wales is:

(a) mountainous, much more so than England. Take a look at an exaggerated relief map of Britain (there is an example at: http://relief-maps.co.uk/assets/map-images/dorrigo030_british_isles_detail_1.jpg) - you'll see straight away that it's not entirely true to say that there is 'no geographic structure separating England from Wales' - the two countries of the UK have pretty distinct physical geographies, and the mountainous areas resisted Anglo-Saxon conquest far more effectively and for far longer than the lowlands of south-eastern Britain.

In the 8th century, a human structure was added to this geographical distinction when the (Anglo-Saxon, lowland) kingdom of Mercia constructed a huge defensive earthwork to protect itself from attack by the (Welsh, highland) kingdom of Powys. The modern border between Wales and England still closely follows this barrier, Offa's Dyke, along part of its length. It wasn't until the 1100s that a powerful new military technology - the Norman castle - was used to project power deep into old mountainous Wales and slowly bring it under English control.

(b) culturally and linguistically distinct from England. As late as 1800, the Welsh language (Cymraeg) was spoken by almost the entire population of Wales, and it may be more correct to say that it's the Welsh people who have been considered separate from and by the English. The concept of the United Kingdom as being a "country of countries", with England and Wales existing as two non-overlapping constituent countries within one nation-state, is a far more recent idea, and it may be that without the precedents set by the acts of union with Scotland and Ireland, Wales would now be treated as a culturally distinct part of a modern Kingdom of England.

Through in-migration to Wales in the 19th century during the industrial revolution and the introduction of homogeneous compulsory education in English by a centralising British state, the proportion of Welsh-speakers had dropped to about 50% of the population by 1900. But alongside this decline in the heniaith (the "old language") came a revival of a distinct Welsh national and cultural identity, including a distinctively Welsh strand of non-conformist Christianity, and a re-invented artistic tradition centred around the bard or poet and the eisteddfod, a national form of literary-musical competition and festival.

Further reading: Williams, Gwyn A. When was Wales? a history of the Welsh (London: Black Raven, 1985).