If Jews go back several generations, either Sephardic, Ashkenazic or Mizrahi/Middle Eastern, there's no way to tell how much non-Jewish blood from rapes and pogroms are a part of every family's tree. In the middle ages, if people who claimed to be Jews moved into a different community or country, did they require them to show documentation like ketuba, brit milah record etc? or did they simply accept them into the Jewish community based on their word? Did they give them a test to see how much they knew about Judaism? I doubt it. After the Holocaust, when survivors would marry and/or immigrate to Israel, did the Rabbis require documentation from them to prove their Jewishness? No, because it was impossible; everything had been destroyed during the war.
The checking of documentation by the Rabbis is a modern concept. It developed after the huge influx of formerly Soviet Jews after the fall of the Soviet Union in 1990, as a response to many instances of fraud by non-Jewish Russians attempting to leave the former Soviet Union.
In my opinion, there should be 2 different standards for aliyah and marriage. I think the status quo that exists in Israel now is fine. However in my opinion, there should be civil marriage there, only between a man and woman, as well. Even a non-halachic Jew must serve in the Israeli army and risk his/her life for the Jewish state. At the least, they should be allowed to marry in a civil ceremony in Israel. If they are killed while serving in the army, they should also be allowed to be buried in a military cemetary.