One reason it feels more significant is that its more recent. The most recent significant Welsh uprising was in the 1400s (http://en.wikipedia.org/wiki/Glynd%C5%B5r_Rising) and the most recent significant uprising in Scotland would have been the final Jacobite rising (http://en.wikipedia.org/wiki/Jacobite_rising_of_1745). It's worth noting that the Jacobite rising was met with extremely harsh reprisals for captured soldiers, although the general populace wasn't treated too badly, and it's worth noting that the Jacobites were predominantly Highland Scots and lowland Scots fought on the side of the English.

Whereas, of course, violence in Ireland has been much more recent. Bloody Sunday (http://en.wikipedia.org/wiki/Bloody_Sunday_%281972%29) was only 43 years ago, the Maze prison (http://en.wikipedia.org/wiki/HM_Prison_Maze) was only shut ~15 years ago.

Basically, mistreatment tends to happen as part of rebellion, and the rebellion has only recently died down in Ireland so memories of the mistreatment are still in living memory.

I'm a little hazier on the details of the conquering of Wales and Ireland but I suspect another reason is the way the English rule was enforced. I can't speak for Wales but James VI and I and the following Stuart kings were joint monarchs of both countries; this didn't lead to subjugation so much as a partnership.

EDIT: Altered wording as per comments

There were also cultural issues at play which have been alluded to by some of the other answers here. Narrowing the focus to Scotland and Ireland specifically, you have to consider the fact that although Scotland had a Gaelic-speaking population, this was confined by the end of the fourteenth century to the western Highlands and Isles. The official language of Scotland was Scots, which is a Germanic language moderately similar to English.

Moreover, Scotland had an actual king, whereas Ireland had Gaelic chiefs/kings in the middle ages but these were effectively deposed by the Normans in the twelfth century and replaced with the 'Lordship of Ireland' which was a title assumed by the King of England. For this reason alone, the Scots were perceived as less barbaric than the Irish - they had 'civilized' government and spoke a language that could pass for English in a pinch. It was the fact that Scotland had a serious royal house that allowed it to assume diplomatic equality with England - the only time that England tried to outright conquer and annex Scotland was when it was bereft of a universally acknowledged king (the whole John Balliol / Robert the Bruce / Edward I situation).

Indeed, the Stewart (later Stuart) dynasty managed to achieve marital alliances of relatively equal standing to those achieved by English monarchs and the two intermarried or even competed for brides. Margaret Tudor married James IV and her son, James V married Marie de Guise who had been sought after by his uncle, Henry VIII.

So really, there are a lot of factors that influenced the differing perceptions of Scotland and Ireland that would have affected the level of brutality and mistreatment meted out to both.

Was one of the reasons England was so harsh on Ireland because of Irelands majority Catholic population?