A suggestion: every month, add one more alien to the missions. ALL missions. So after day 180, there are +6 aliens to deal with, and +8 after day 240. We can even say that it starts only after 60 days or so, so we'll be at +5 after 180 days. But currently, something like 15 aliens spread out over a full map while I can bring 16 soldiers concentrated in one location? Of course that's not a challenge, not even on Commander.
Sure, the enemies become stronger, but so do you: you get better soldiers, better defence, better offence AND more soldiers to bring to the field. It's a bit too easy with 16 soldiers fully decked out if the aliens don't get any kind of advantage.
Or perhaps increase the chance to throw grenades with each passing month: wounded soldiers can be killing for a campaign.
Perhaps add poison gas to the game, which dramatically reduces the healing recovery time?
Reapers need to be more terrifying. Sure, they hurt when they get close, but they never get close enough to attack. Perhaps add more movement speed to them? Reapers need to be like "Oh shit, full fire on that unit!"