We learned from Firefall that designing a shooter for PvE and PvP simply don't mix. They might as well be two very different games. Ember is being designed for PvE. Later, if we add PvP, it will be very different from the frames you play in PvE. But that's a big if.
Perhaps if you explore a different method of delivery; in your current model it has been observed that the frames are the centerpiece the player focuses on. However, if you shift that focus to a more neutral point, say the pilot, and differentiate between competitive PvP components versus say Warframe components (amongst others such as Industrial, Civilian and "Other") you gain that lateral leverage you need in the progression system.
It is generally agreed that this would entail a larger asset and development line for the initial build; yet this can be mitigated with the use of staged content release so the development can come in waves of finished deliverable content and hint to future builds. I would venture that the pilot's skills would allow them to modify their core piloting abilities to say unlock future content and frames as much as vehicles, LGV's and the like. In the integration of armies/factions this would facilitate modes of specialization players can take on that both fit the roles of various leadership as well as being able to continue to enjoy the game regardless of it's level of interaction.
Let's explore for a moment the idea that a catastrophe initially befell the centerpiece of the initial release playable faction(s). Anything that reduced their operational technology levels well below the normative expectation of a thriving society. We would see the emergence of a unique and wholly separate production and restitution of that technology but in a new way. Similarly, we are confronted with a dev decision not unlike Daniel Erikson, and the dilemma on delivering the Star Wars ideology and lore in a fun and engaging way. In this he decided on theatrical movie like fighting modes that would highlight the actions over the player interactions. In PvP this translated to MACRO's and Botting. The decision to give 'space on rails' was an old tool but the delivery was not well received at all and the subsequent attempts to revitalize space combat PvP or PvE is hard pressed to return to launch numbers.
Now in design terms, we are really discussing that age old catch 22, if you do nothing and appear a genius then it's genius, yet if you do something, anything; it can begin the end of your career depending on how it is received by the interested community. This is the age old tale of ever title launched to date. Nevertheless, to deliver on those promises we mulled over and watched (enter Extra Credits) there should be some form of dynamic focus that will allow for progression and participation in both aspects of the game seamlessly; or as close to the idea of it moderation and arbitration could provide. Sometimes PvP is it's own beast with regards to feelings and personalization. Yet with a well dicated ruleset and clearly defined crime and punishment system those issues quickly evaporate to competitive standards.
Take the MoBA competitive and Star Craft real time live action simulation. Each offers a completely defined set of achievable content, direct and balanced competitive matrices and they work to ensure the competitive edge is maintained throughout the creation of the content; i.e. powers and abilities that if earned highlight the character model and not act as balancing systems directly for all content.
At this point, I am certain you have joined equally versed conversations on this subject to ad nauseum; yet I implore you to consider the benefits of attempting to create this single advancement in the gaming industry that is so desperately needed. With the joining of competition and personal responsibility the game can become more than just a niche, it can break that mold. Ya'll were so close with the last model, and the balancing and rebalancing was IMHO right out. Skill and bot/hack protection are where things fell apart with aimbots and hacktools.
Any, whom, I tend to wax on from time to time. This is very exciting and I look forward to the core mechanics that will be offered this time around; at the very least, it may be a great side game afterall...