As a disclaimer: I'm certainly not a professional writer by any means, and this is just for fun. I hope no one gets offended.
Don't get me wrong, I liked Merlin. I watched all of it, the latter several seasons basically as it came out. But I have to admit that, for all its strengths (interesting relatable characters, attractive talented actors, and a cool premise for a popular storyline), it also had a lot of glaring weaknesses. I think the thing that always makes me the saddest is how much potential that show had, and the fact that that potential usually never went anywhere.
As a comparison, I loved the two new Star Treks. I think I once explained to someone that it was as simple as basically everything I wanted to happen happened, and the things I really didn't want to happen didn't happen. In comparison, it was often the opposite with Merlin. Now, I'm not talking about things like "which OTP should get together" or that I had a specific plot in mind, but more that a lot of the plot threads started with potential and ended up taking the easy way out--often a way I had foreseen and was hoping we could avoid for how easy/cheesy/OOC it felt to me.
Here are what I think were the main weaknesses in Merlin, especially starting from S3:
- underdeveloped/2d/static/black&white characters
- use of common/cliche plots points with predictable results
- insistence on trying to match the traditional story (despite starting off deviating a great deal)
- disconnect and lack of communication in the writing between episodes
- lack of appropriate character motivation for villains and hand-wavey explanations for personality changes
- attempt to change to being non-episodic not hugely successful
So, what if I had gotten a say in the writing for Merlin? What would I do? Well...
Develop Antagonists:
- have more inner struggle for Morgana in S3 about having turned to evil, hurting Arthur, killing Uther, etc.
- more backstory for what happened to Morgana with Morgause between S2 and S3 to make Morgana suddenly willing to kill people
- either have Morgause be a black and white villain, or actually develop her sympathetic side after S2
- explain about Morgause being Morgana's half-sister and Morgause's parents/Morgana's mother
- have Uther show more of his doubts and/or willingness to use magic for someone he loves
- have Morgana return to the "good" side after a season or so of evil rather than making her the primary villain forever despite her having weak motivations
- had more of the villains last for more than an episode, and give them some more storyline
Develop Protagonists:
- develop Igraine's storyline more clearly and have Arthur learn the truth so that he has to deal with it
- involved the knights with more plotlines (e.g. in the last season, there was an episode where Merlin was arrested for treason by possessed Gwen and none of the knights even tried to protest. It felt kind of OOC and like we missed a big chance to develop them.)
- generally gave the knights more focus--e.g. had episodes where Merlin has to go on a quest with a knight, or where Arthur takes two knights to something Merlin isn't around for
- had Merlin heal Uther of the magical affliction as Dragoon, causing Arthur to have to hide the fact that he used magic to heal Uther
- had Merlin reveal his magic earlier so that Arthur has to struggle with his feelings of betrayal/etc. and his not wanting Merlin to die
- kept Mordred good and/or gave him a less predictable/cheesy reason for his betrayal, or even just a less obnoxious girlfriend. Alternatively, he could have just gotten angry enough to tell Morgana some crucial secrets but not joined her. (basically it felt OOC for Mordred to join the person who represented everything he hated just to get revenge on Merlin for getting his really bitchy girlfriend executed
- made Gwen more able to contribute to the story
Relationships:
- kept Arthur/Morgana and Merlin/Gwen (Merlin/Arthur? Gwen/Lancelot? something different, basically) rather than trying to force Arthur/Gwen
- developed more on the Arthur/Gwen/Lancelot love triangle (if Arthur/Gwen must be a thing) instead of killing Lancelot immediately
General Developments:
- went deeper into the Aithusa/Kilgarrah relationship, and potentially had Aithusa not just make Morgana more evil
- given more info on dragons in general, such as how Aithusa managed to survive as an egg
- kept some of the magical items (e.g. the Fisher King's water glass) and plot threads for more than a season to tie distant storylines together
- further explored the Old Religion and magical creatures in general (e.g. the Sidhe, the dwarf on the bridge, etc.)