Every combat system goes through these problems. Eventually the Community will find the optimal combo or weapon skill even if they did adopt your suggestions. I rather the developers streamline it themselves and make it accessible to all of us and not just the people who read up on games. While i do not think the system is flawless, the more i play with it the more tightknit and well designed i find it.
Pre 1.20. i think Lancer had the most diverse and balanced set of weapon skills. And i thought MRD kind of had a crappy set of weapon skills that felt like clones of each other.
Leveling up as a Mrd and just hitting 50 today gave me some time to learn the ins and outs of abilities as they were introduced. Its true that your combo selection is set in stone for the different scenarios, but the fun and decision making comes from setting up the combo with your fellow party members. The combat Scenarios that you get into this game are always black and white as spank the monster while the tank has agro, especially if you're going through the beastmen strongholds.
Before a large focus of this game was AOEs, and it was initially shocking and frustrating to me but now i'm good with it because setting up whirlwind takes some thought and is interesting, even though weather or not to use it is no brainer.
There are a lot of times when i do a Raw non comboed WS and this is mostly because my cooldown timer is down and i have tp to burn before i end up wasting it. The trick to this is picking which one and planning ahead so that you do not impede your combo action in the future. I especially like doing Whirlwind raw even though the cost is 3k tp, and that's because i had a good rampage going and i dont want to lose it because that effect outweighs the damage of a combo. Or Maybe it is, if you are going to be able to finish the fight/save your party for it.
There is another way to gain TP and that is through Quelling Strike. If you use it on your combo opener or a raw WS, then it just reduces the cost a bit, but if you use it on your tp free follow up attacks then you get free tp (assuming that you hit ). Problem with this is if you're trying to keep hate, the free tp maybe isn't worth sacrificing possible hate for. Another Decision. What buffs you use to power up specific attacks in the string of the combo are also another thing to consider.
I've been focusing on trying to get my raw auto attack to be more proficient, because it seems that is the focus of MRD compared to the other Melees. We're slow hitters and TP also gains slow because of it, so how i treat my weapon skills matters. Its a stark contrast to LNC, which combo's up the butt and always has TP, ways to gain tp, and ways to spend tp.
So in conclusion, the current system the way it is is easier to balance. Having something more complex and harder to design does not mean that people wont eventually find their 3 combo's to end it all. There are bigger things in battle to think about.