I'm a fan of long campaigns, and one of the features - or rather quirks of design - I enjoyed about X1 was the pseudo-infinite nature of the invasion. So long as you maintained control of the skies, you could play as many rounds of UFO: Breach & Clear as you wanted to. Indeed, that's often what I did, building a roster of dozens of elite soldiers with Sentinel armor and Mag weapons before I even entertained the notion of starting operation Endgame.
Because of this I'm cautiously optimistic of the ticking-clock added by the Alien weapons platform. Thematically it does a very good job driving home the aliens superiority, and the added time pressure should prevent a soft-lock situation where you don't have the capability to engage or capture any of the UFOs spawning in later months. However, as things stand now (I understand that we're in very early development, and that everything is subject to change) it feels like the game is running on a set schedule, without much room to play longer if you wish. Research the tech tree on time to stay ahead of panic, then launch the endgame seems like it will be the only strategy possible.
Thus, I propose this; At some point generally in the middle of the game, UOO-1 is removed. Perhaps Dr Snidely had you test the tactical viability of the aliens jumpdrive by inserting an alenium-augmented Nuke into UOO-1. Perhaps you manage to board and capture the device, again as humanities first foray into using the jumpdrive. Whatever way it's implemented, there is no longer a hard time till extinction. The invasion then changes and escalates, but in a way that the player can fight off indefinitely.
You might ask why the aliens would let go of such an insurmountable advantage, but I remind you that a key thematic point of X1 was that the Aliens were evaluating us for assimilation, not attempting our extermination. Indeed, if they wanted us dead they could simply tow some large asteroids into an earth-crossing orbit and wait.