I am all for this new rules change and am happy to pay the minor flavour costs to obtain a better overall game. With only one copy of each card the rules changes are of minimal effect in the cube compared to other magic formats. Within the cube it has only really two ramifications, making clones no longer Hero's Demise in blue and allowing multiple copies of same name planeswalkers in play at the same time. The latter in particular I am fond of as it means the first person to resolve their Jace, Elspeth etc is no longer vastly ahead even if they have made a weaker version. Typically in control mirror matches Jace Beleren was the best of the Jaces as you can cast him soonest. This in turn means they have to spend four or five mana on their Jace that only serves to kill your Jace from which you have already obtained value. Now with the new rules you can make your Jace Beleren first and I can still make mine and use it as intended. While you may have been getting activations a turn or two earlier the fact that my Jace cost more implies I will get more value from my activations and be able to catch up somewhat. It also means we both have much more choices to make as we both have a Jace rather than both not having one. Choices are good, they allow you to outplay people and they make for more fun and involved games. You get to use the card in your deck for its intended use, perhaps you were playing Jace the Mind Sculptor to set up your miracle cards and without the use of his abilities your deck has way more overcost spells and becomes rather unwieldy. Having deck synergy and design disrupted unintentionally by cards in this manner is random and detrimental to the game which the new rules changes have ironed out. You will still be forced to consider to drawbacks of playing two or more copies of the same walker in your deck however you wont have to worry about those from your opponent.
As for the changes to how clone effects will work I am also very pleased. Being a legend in the cube was a large drawback and made a lot of cards unplayable. The main culprits in ruining many legends are Phantasmal Image, Karakas and Phyrexian Metalmorph and the new rules will stop two thirds of the problem. The best example of a card made unplayable by clones is Thrun, the Last Troll who was supposed to be incredibly hard to deal with, in particular by blue however in the cube blue found it easier than any other colour to cope with him. The clone cards are still very good and won't lose much value compared to the legends like Thrun who will gain an awful lot of value. If they make a big scary legend you can clone it and have the situation equal as if you had killed it, just more complicated and interesting. A trade off where one group of cards lose basically nothing from their value and playability while another group vastly grows in these areas is a good trade in my books.
As for flavour concerns I am not worried, I can look past the idea of a Sword somehow being a combat aid to a dog and so I will be able to deal with this too. I appreciate not everyone has the same indifference to flavour in which case its a good job you are into cube as you have all the power to play whatever flavour based rules you like. I also appreciate that certain cards will become far more abusable in formats where multiple copies are allowed such as Mox Opal and Gaea's Cradle. This may incur some bannings or meta shifts and card value swings but it is still a good thing to do for going forward with magic.