Actually, I can see a case for SAM.
It's only the combo finishers that have unique effects, other than the two 2nd GCD's each applying a minor buff, so you could just have them as three buttons that cycle through the combo like Continuation, syncing up the first and second button presses so that you can switch between them on any given GCD, and apply the relevant Sen when completed. Meikyo Shisui could then fix each button at the last of the sequence until it's spent. My only issue is the discrepancy between the 3-combo Getsu/Ka and 2-combo Setsu finishers, and whether or not that would be too much to coordinate on the fly or if it would simply take a lot of getting used to.
This could then make SAM's combo system markedly different to the other melee and free up space for some more focus on Hissatsu skills.
I'm still not convinced about MNK and/or DRG though.
You say "the issue is it's designed that way" but then, it IS designed that way. MNK is 100% based around it's combo system, with each discrete GCD having it's own positional, it's own unique effect, and two skills to manipulate your combo progression. Your whole focus is on what part of the combo you are in on any given GCD, and muscle memory is very important for it.
I am all for making changes to some jobs, like SAM, to mix things up and create more variety between jobs, but in MNKs case, it's very much an intentional design choice, and by removing it's combo system you remove part of what makes it's specific job identity, and you also force MNK players to be constantly glancing at their hotbars to check what part of the combo they're on instead of relying purely on muscle memory. While this would be an issue for SAM only every 2nd or 3rd GCD, this would be an issue for MNK on every single GCD, while adjusting positions at the same time.
DRG is it's own beast, and unfortunately I haven't played it enough recently to be familiar enough with it's nuances to to make a solid case. However I know from optimising my MCH bursts lately that counting which Heat Blast you're on is essential in not clipping your GCDs (you need to hit 5 Heat Blasts and know when your 6th GCD is up so that you can get a Split Shot/Drill/Anchor in your Wildfire window as well) If you lose count and you go to hit Heat Blast as your 6th GCD again, it will fail, and you will clip, and you will definitely not fit a 6th weaponskill into your Wildfire.
You're watching your hotbar like a hawk at that burst moment, in order to hit your GCDs smoothly, and it requires markedly more focus than your 1-2-3 combo does. That's fine, it's a burst window, but it's not sustainable 100% of the time while also dealing mechanics.
But my reservation is that doing this to DRG's entire combo system, would turn it's entire rotation into this same GCD counting, hotbar watching exercise that MCH's Hypercharge/Wildfire window is. Instead of allowing your muscle memory to keep track of your combo progress, you're constantly counting "1, 2, 3, 4, 5, 1, 2, 3, 4, 5..." and/or constantly staring at your hotbars instead of the battlefield.
So I would say, in the interest of keeping jobs different and interesting:
Consolidate SAM.
Keep MNK as it is, it's combo system is it's signature.
DRG is a beast of a combo system and if it needs consolidating, it also needs some concessions elsewhere or some kind of rework to allow for it.