Vortex's system is situationally inferior as any time you want changes to take effect you have to 'redeploy' your mods which takes a bit of time and can, if Vortex glitches, leave 'remnants' of disabled mods until you use the 'purge' option which can cause its own issues if it deletes something it shouldn't.

Since it's all handled when the game is ran, once you have a mod extracted installing and uninstalling is as simple and quick as ticking a box. MO2's system allows for much quicker and reliable 'mod swaps' than Vortex and especially NMM. Vortex allows you to launch games/tools externally which tends to be more compatible. However, that can also be a benefit since you can swap profiles much quicker or even revert to a completely vanilla game without changing anything. This is usually acceptable, but it can create issues on unusual setups (New Vegas on laptop battery consistently fails to launch for me). The practical differences are MO2 needs to have the game launched through it. Mod Organizer 2 uses a 'virtual file system' to mod your game, Vortex creates dummy files that link to the originals. Mod Organizer 2 and Vortex are the big 2 managers.

Fallout mod manager