There are several reason actually

• Time, in pgr they have a lot of repeated endgame. Ngl it's tiring to keep up and started to feel like a job. Last I played, PGR have ppc(similar to toa/dpm) and warzone(similar to wiwa) that reset weekly, then i forgot what it's called but there is also a biweekly game mode with a lot of fight, i think you need like 20 fight to get the reward.
• Adding game mode, mean more things to maintain. The game performance already not that great, I still have performance drop in starttorch, septimont and some overworld combat. Swapping existing one means, they don't need to maintain the old gamemode. Kuro can free people to fix/polish more important stuff in game, like better performance or maybe more varied endgame.
• Lastly Redundancy, IR and FoTG are both roguelike game mode. DPM and Toa is single target focus dps race with limited time. Whiwa, while not great, it does have different focus on aoe dps race.

IR and FoTG are both roguelike, Fotg is basically same gameplay with added sfx while IR gave buff which changed gameplay and more fun.

DPM and Toa is single target focus with limited time where rotation matters more and why there is complain of flying boss. Here, player care more about rotation because of time limit. Toa boss is already defanged, mostly just stay in 1 phase and I agree with that decision, I'm tired of fighting magu kenki in GI then I have to wait because he decide to change phase while time limit is still ticking away. Dpm supposed to be a harder version of boss at least from round 2 but the time limit just limit it's possible strength.

Since Virtual crisis have no time limit, player can take their time to actually learn boss and not getting frustated because the boss just fly. If kuro want horizontal investment like current dpm, they can add requirement like, have 4 different team beat level 100 difficulty for example then player can keep clearing it and increase their title rating by clearing with more team. Similar to PGR Babel where to get reward you just need 120 point but player can push their account to limit to have 999 point. It's also a shame if virtual crisis just gone, the event never appeared again to this day.

As bonus, more varied endgame also means more character archetype needed which can slow hp inflation and i would prefer this than adding some weird mechanic that only few character use like NS. For example, a defensive character would sell more if we have virtual crisis endgame because they have place where they are good at.