I'm not sure that a Protestant Ireland would change all that much actually. While the island’s Catholicism was certainly a factor in the English (and Scottish) attitudes towards the place, the movement towards the crown asserting itself began before the break with Rome and was for political and strategic reasons as much as anything.
Whatever religion Ireland was (and it’s unlikely that the whole country would be converted all at once anyhow, so there will still be Catholics in Ireland even if the majority are protestant), the English crown will still see it as a strategic threat; to impose control they would still need to replace some of a aristocracy and stamp out a range of traditional practices, which will naturally cause rebellions. Of course, it’s vanishingly unlikely that whatever reformist religious doctrine that took off in Ireland would be the same as that in England, so there would still be religious differences. Irish Protestantism would be as foreign to Anglicanism as Calvinism was; If you’ll excuse the pun, Protestantism is a broad church; look at how, during the 1640s, Anglicans, Independents and Presbyterians all took the opportunity to victimise the other; or indeed, how Henry VIII suppressed Lutheranism during his reign. I think there will also still be plantations, although now the conflict will presumably be Anglicans vs *Presbyterians rather than the OTL sectarian divide.
There will still be big differences; I think the paranoia regarding Ireland and the Irish on the mainland will be far less severe if the Irish are broadly seen as protestants, and there’s a hell of a lot of scope for Hiberno-Scottish religious cross-fertilisation. Maybe this is a TL where (unfortunately for the locals) the Scots take a greater interest in Ulster during the 16th and 17th centuries? It’s worth remembering that it in an irony of history, was one of the most staunchly Catholic parts of Ireland until the plantations; ITTL it may well be the last Catholic holdout on the island, and so a natural target. The old Anglo-Irish aristocracy might survive a bit better ITTL f they manage to get on board (and I think they would, as the most likely conduit of reformist beliefs into Ireland). IOTL the Irish were never able to present a united front in the face of the Crown and ITTL things will be even worse, as London will be able to play off Protestant Lords against their Catholic counterparts; there will also be knock on effects on Europe more broadly, as France and Spain’s favourite source of foreign manpower has just potentially dried up.
So an interesting TL, really. But what's the best way to get there? Any indigenous Irish protestant movement is going to have to get started early and spread very quickly; prosletysation from the rest of the British Isles was always a complete failure, and as other people have observed once England and Scotland sever ties with Rome, particularly the latter, then it’ll be very difficult to get the Irish to do otherwise.
There are two ways to do this, I think; you either set up an Irish movement that predates Luther (inspired by the Hussites?) or you delay the Anglican break with Rome. The latter seems more plausible, but isn’t enough on its own, but butterflies are our friend there!
So, PoD; 1528. Everyone in the Royal Court is quietly relieved when Katherine of Aragon dies from the sweating sickness that’s sweeping the realm, and King Henry is able to shelve his plans to annul his marriage. After a polite interval, Henry marries Anne Boleyn the following year, and life continues as normal. Nobody much notices that thanks to some helpful butterflies, the Earl of Kildare is able to scrape together enough cash to send his son to study in Paris, where the young Thomas Fitzgerald (also known as Silken Thomas) becomes friends with a scholar named John Calvin.
The two are separated when Calvin is forced into hiding, but retain a correspondence even after Fitzgerald returns to Ireland. His rebellion against King Henry is butterflied away for the time being; instead, Fitzgerald succeeds his father as Earl and spends the next few years quietly promulgating his heretical beliefs amongst the Anglo-Irish aristocracy, getting his cousin the Earl of Desmond onside amongst others. For a brief time, Dublin is a haven for reformers fleeing persecution elsewhere, and men like George Wishart begin spreading the new doctrines amongst the local clergy.
Henry still breaks with Rome- the uproar over his execution of Anne Boleyn sees to that- but his eye isn’t drawn to Ireland as quickly as IOTL and there’s another five years of peace. Finally, in 1540 Henry decides to interfere, and uses Fitzgerald’s evident Lutheranism as a pretext to strip him of his title as Lord Deputy and summon him to London. Believing that he will be executed, Fitzgerald renounces his allegiance to the King and rebels, quickly getting his cousins the Fitzgeralds of Desmond onside as well. The rebellion is far worse than OTL’s “Silken Thomas” affair of 1534, and has more in common with OTL’s first Desmond rebellion, but spread across most of southern Ireland. Resistance is eventually crushed by the crown, which suppresses many traditional gaelic customs; at the same time it creates martyrs out of the two Fitzgeralds, who are executed in London.
The Irish reformation proceeds in fits and starts over the next few generations. The persecution of protestants under Queen Mary gives a serious filip to the movement, and by 1560, when the newly-crowned Queen Jane starts aggressively asserting control over Ireland, Leinster and Munster are the centres of Irish reformism, with broadly Calvinist ministers preaching to their flocks in Gaelic.
Thoughts?