In ep 12, from 13:20 to 14:40, the recording of the "ancient aliens" that visited Earth before begins playing, while Ichika is inside the federation probe being carried upwards into orbit:
I wonder how long it has been, but thank you for finding this.
I made an emergency landing on this planet after my spaceship had trouble and was saved by someone here.
Before I knew, he meant a lot to me. But this is a remote planet where contact with the locals is forbidden. Help will soon be on its way.
I imagine my memories on this planet will be sealed away to mantain secrecy .
But... I wanted... to leave behind the memories I had with him, no matter what.
Even if my memories faded, even if I couldn't remember, I wanted to leave something behind. Thank you for finding it.
I pray that at least my memories will live on with you.
Please don't forget.
Comparing the text above with the story of Onegai Teacher, if it was left behind by Kazami Mizuho, it should be before she is recalled into HQ and everyone's memories are wiped out. One thing that does not click is that it seems like an accident. Mizuho came to earth on an observer assignment (contrast with Ichika, that came on a "tourist visa").
Some of the alien's technological similarities I pointed out in the other question are then justified if they are the same universe. You would pretty much expect warp nacelles in any Federation ship if it is in the Star Treck universe, for example.
But the final evidence is that the above text is voiced by Mizuho's Seyuu, Inoue Kikuko. Anime News Network has credits for her as "Misterious Voice (ep. 12)".
The production staff for both series is very similar and they share the same character designer.
So they probably are the same universe. Whether any of the characters is a descendant of Onegai ones, is better left to the realm of speculation. But it could explain why Ichika has memories of Mizuho's recording.