As a veteran melee player (with 1500+ hours of melee gameplay) currently I see several flow-breaking issues with mele 2.9998
#1: Unmounting archwing in open world areas (since there is no other way to do so) forcing you into melee mode. It is more of the Archwing issue than the new melee system, but does break the flow especially with slow weapons and "use LMB as melee" option toggled.
Next one is related to the transitioning into the new combo system from the current one. Phase 1 was advertising for "instant gun to melee and melee to gun swap", however the "LMB as melee" just brakes everything down. RMB in theory should sway you to the gun mode, but it is also a trigger for the blocking combos, so it waits to swap until the animation is finished, and that is several seconds even with the faster weapons. Even more annoying is triggering the block-combo with RMB will force-swap you out of the melee mode, once the animation is finished. The wolves are sated and the sheep intact, but after having to swap back over and over again I'm not even taking any guns with me on the melee runs anymore. Doesn't worth the hassle with constant unintended swapping.
Speaking of melee-only. Equipping codex scanner/mining cutter/fishing and then unequipping it with the same hotkey will let you block with RMB if melee is your only weapon, however unequipping it with a melee swing will change RMB to swap back to whatever gear it was until the end of the mission, thus making blocking or melee-glide inaccessible.
I couldn't find "peaceful" way to switch into melee mode without having go through the swing animation. Sometimes I would like my melee out to block, but swapping on the last second and having to wait for the animation to finish makes me take the hit anyway, since blocking is disabled while swinging.
The new system does feel great for gunplay with some melee splashed here and there, however with all the flow-breaking hitches it's not even close for the opposite. If you want to play a melee-based playstyle now, going sword-alone is the only option to avoid all the hitches with unintended behavior and conflicting keybinds.