The issues I have with the endings, and the story in general, are:
1. V is dying, and the character acknowledges it very soon, so doing anything that isn't related to finding a cure/solution is immersion breaking IMO
2. V will feel worse and worse the more you progress through the main story/major side quests. This isn't an issue by itself, but see other points
3. V dies or leaves Night City after you beat the game. This isn't an issue by itself too, but it becomes an issue if you combine it with other points
4. Literally, in the only moment V is pressure-free without the relic, you can't explore Night City because Watson is in lockdown. Come on, seriously?
IMO, the only and best moment to do side stuff with the current plot is to not trigger the Arasaka parade, and do everything you want before that, but many interesting side stuff comes only after you progress further in the story (Panam, Kerry, Johnny's gear etc). Probably, speaking of major side quests, you can do only Judy's and Alt's stuff before triggering the Takemura call for the parade, but I'm not 100% sure.
I think this is very, very bad design for an open world videogame, probably the worst I've ever seen, and it's a shame because it's a fantastic game overall. But you can fix bugs, you can implement crowd AI, you can rebalance stuff or add features, but the story? I don't think they will fix that, I don't even think they'll ever acknowledge that as an issue.
I'm curious to see what they'll do with DLCs, as they will have the same problem: if V is dying, doing everything that isn't related to finding a cure is immersion breaking for me, so, if they don't let me play the dlc with an "healthy" V, I probably won't buy the DLCs.
TLDR: the endings are a problem because they mean there isn't a single moment that V can explore Night City "freely", and that's bad because V is the protagonist of an open world "almost maybe rpg" videogame. This may be a problem for future DLCs too