What a great question ctg.
I'm not sure that I would change too much, especially keeping in the back of my mind the restrictions of television.
Much as I'd like to see epic battles with countless knights hacking away at one another, I don't think it could be done.
So the first and biggest thing is getting Merlin out into the open, with Arthur if not with anyone else. The two of them have this bond that has grown over 8 years (allowing for the time passed between seasons 4 and 5), if Arthur will not accept Merlin for what he is then there is no point in the show.
With the above happening it allows Merlin to move from being the magician under cover as a servant to trusted adviser. This in itself would open things up.
Rather than having plans brought into effect week in week out - generally Morgana setting a trap. Arthur walking into it, all looking lost saving the day, bring in a few fresh ideas - drawing on bits from Arthurian legend/popular tellings - let's have Pellinore and the questing Beast, perhaps a bit of friction within the kingdom, bring Lancelot back from wherever.
Don't end it suddenly, rather build it, perhaps having time pass, the quest for the Holy Grail over a number of episodes, Galahad, and Nimue the female force that will ultimately remove Merlin from the story.
Phew, and I'd like to see Arthur have a long reign will the fall coming more than a few years of his ruling. We want to see that he is a stupendous king, legendary in fact...