I don't know that our Noll was really into re-settlement as such. He was just concerned with turfing them out. Where they went, if they went and if they survived when they got there wasn't really his problem. The places he 'ethnically cleansed' were places like Drogheda and Wexford, prosperous, fertile and on the East coast. Where the evictees ended up was further West, and stony and infertile by comparison.
He couldn't find everybody, true, but armies don't have to. They simply have to destroy or dislocate all lthe support mechanisms that allow people to live independent lives. If you are a farmer you need the peace and the time and the manpower to harvest your crops and husband your livestock. It doesn't take much interference to make this impossible. Controlling the towns also meant control of commerce, the movement of people and goods, shipping and overseas trade.
Cromwell is not universally revered in the UK - many people see the Cavaliers as much more likeable, if inept. Cromwell is principally respected as someone who upheld the rights of Parliament against Royal dictatorship. The fact that he in turn had his own problems with Parliament is often overlooked.
As to why his reputation should be so bad in Ireland: Scotland and Wales were and still are predominantly Protestant. Ireland was and is predominantly Catholic. There was a religious dimension to his treatment of opposition in Ireland that was (largely), absent from the English Civil War and later actions in Scotland.