Any way for Wales (In the form of Gwynedd, or whatever you want, really) to rule as an independent country, or ruling a larger part of the Isles?
Looking at times from 1000 on to 1900. (So no independent Romano-British...)
From 1,000 A.D. onward? Highly unlikely. The last real chance they had for that was in the mid 7th century, when Cadwallon ap Cadfan of Gwynedd almost destroyed Northumbria. By 1,000 A.D., the English were too entrenched in England to be ejected from any significant part of it. And once the Normans get in there in 1066, the chances that Wales is going to remain independent drop to zero.
I suppose that if the Saxons win at Hastings, there is a possibility that an independent Wales may survive, very much in a client relationship to England, to be sure, but still independent. The Saxons had, by that time, pretty much given up trying to conquer Wales and accepted Offa's Dyke as a permanent western boundary for England. But, of course, once the Viking threat is removed, some Saxon king in the late 1100s or early 1200s might decide to renew the wars against the ancient enemy. In that case the Welsh people probably don't survive at all in recognizable form, as the Saxons would probably engage in ethnic or cultural cleansing there, as they apparently did in all the other areas of England they conquered. Probably Welsh, like Cornish, dies out as a spoken tongue sometime in the 18th or early 19th centuries in that case.