Has it been answered ingame how the aliens has reached earth? (i ahvent been able to get any payment accepted to get the gae yet) Have they allways been in close proximity? Did they travel here in a big great space fleet (like in the series "V")? or do they have an Origin planet taht they travel back and forth to? I'm guessing it hasn't been revealed. One way to break away fromĀ“the original X-com could be to not have a base reachable from our planet.
Lets say that the Aliens use "jump gates" to cross large expanses of space. They got one in their system and one or more recievers in ours. That way they dont really need a master base in ur system or a mothership. Say they have 50 or so recievers that are big enough to accomondate the alien vessels traveling through them but small enough that they are difficult to detect and closing one doesnt really do anything to stop the flood. (We are also assuming that the launcher gate is bigger and a sort of master system, so that if you destroy it it wont be just a simple means of replaceing that like it is replaceing the reciver gates)
Through interrigation you get the means to either trick the master gate to open up a gate or information on when a gate opens so you can ride on the backdraft to the mastergate or whatever.
Once there you realize that you are on their moon. The jump gate master system is a superstructure built into the very core of their orbiting moon. (assuming their moon has a synchronozied spinn/roation just like ours does you will have their world above you)
Instead of ending the threat by destroying their race or something you can postpone everything by sabotageing their jumpgate causeing a cascading effect as you take the last jump out. Then you mop up the remaining spaceships, research as much of their tech as possible and convert the reciver gates into a stellar defence network with monitoring to detect if they become active again.
(Sets it up nicely for a sequel ^^)
PS. hmm a bit more work and i can make that into fanfiction=P DS.
PPS When i think about it it does sort of remind a bit about X-com apocalyps... but that was interdimentional travel and you killed them. and that game had the most dissapointing finishing screen i ever recall getting. DS.