Well this isn't the "bad anime" thread so I'll keep it brief.
1. Kouichi is a pretty bad protagonist-While he mellows out over time, he starts the series as this complete jerk bashing up both allies and enemies with the LINEBARREL. At first, I actually liked this because honestly, that is how a teen in high school would probably act with a giant robot. But it comes off as him completely inept to make rational decisions.
2. This show seems to not know what it wants to be-Is it a mecha? Romance? Harem comedy? Tragedy? Philosiphical explanation of multiple universes? Plus, you've seen all this before in considerably better anime. And the plot likes to take breaks for fanservice at considerably annoying times.
3. Ali Project does the opening-Nah, this isn't really a reason. I just don't like Ali Project too much.
4. The ending-Obviously, I'm not going to spoil what happens but it was obviously rushed. It's considered one of Gonzo's worst endings among viewers.