Great question!

If you think about it, the mechanism of the time travel here is very similar to the one in Back to the Future. The travellers are the only ones who retain consciousness after travelling in time. If you pick up the hint from Zero's own class (as a professor and as a student), you see that they mention a new reality is created every time someone jumps in time. What's new in this movie is that you CAN interact with your past version, more versions of you can occupy the same "reality" and, by judging from the cool ending, there can be predestination (your future caused something in your past). Here, Zero had no memory of being visited by his future versions (from his perspective) until he was the one travelling in time from 2011 to 1991. This was cleverly disguised as a hallucination and then as a drug-induced dream. Another difference is that the traveller has to control the destination of the time travel jump with feelings. This sounds a bit off for hardcore SciFi, but it also happened in "Somewhere in Time", which also had some sort of predestination in it.

"Also, what other conceptual problems or limitations stood out to you?" - the matter her isn't about conceptual limitations. It's about having no idea what would happen if time travel were really capable. The limitation is our own knowledge. How can we say the movie broke "rules" if we don't have any yet?

For me the most intriguing concept is - what happened first? How did the retro-causality start? We never see in the movie a reality where there was no time travel - what would have happened in THIS reality? The Humiliation he suffered as a college student only happened because his future (astronaut) self orchestrated it. Just before gave the "Google" hint to Sandra, who then sponsored him and allowed him to come back in time in the first... I mean, last... place :) There are only two realities - the one with one Zero in 1991 + awful 2011, and the one that starts and ends the movie - in which there were two version of Zero in the past.

Now, a thing that fascinated me was Helena. She always loved the nerdy guy. By the time she pounced him, they had been around each other for over one year - long enough to fall in love with some due to content rather than package. When the movie started, she had already spent 20 years away from him, just waiting for the time to see him again. She did live through 20 years after she last kissed the Astronaut Zero. The Astronaut Zero had last kissed here a few minutes earlier from his perspective.

I think there's a lot of character growth (not only development, but real growth for Zero's character) here built-in this SciFi/Rom-Com/Musical movie.... And it worked quite well