As long as the option of pay-to-skip doesn't impact possible lore-rich quests in the future (that is to say, as long as the financial incentive of making bland quests to drive up pay-to-skip quests sales doesn't overtake the incentive to make good quests) then there shouldn't be an issue; it would just be another way to play the game.
The concerning part is that the pay-to-skip is paid in the first place. If it was meant to attract new players, then being offered more microtransactions could make them even more likely to turn away, because players coming to warframe have probably already seen many examples of pay-to-win games that they can easily immediately classify this game as, regardless if that's true or false. It's the first impression that matters, and seeing a banner to skip the quests for $$$ is probably going to be just another turn-off for them.
Let's suppose another method: making Duviri Paradox the springboard into the game in its current state by allowing access to the game in the state after the new war with the drifter (and without the operator) and a notification stating that you can go backwards in time through the transference room. Basic quests leading up to the new war can be strung together on a timeline with entry points at Vor's Prize and the New War to give some direction of what the main story is (which is somewhat lacking early on anyway). This would allow full access to new content, but whether they can do it with that gear is questionable.
That's the real issue with paying to skip quests. The real grind was always setting up to do most quests these days, and paying to skip that is already available. Although a solid catch-up mechanic would clearly be very good for new players, I'm uncertain that this would do what's intended. Instead, maybe just adding better early-game credit/endo farms and changing the drop rate + upgrade costs of essential mods would be a better approach for getting new players up to speed. If the main storyline can be more easily seen in a timeline instead of in the format shown in the codex, that would also be a great addition.
