Difficult to think of a context when anyone English would say "He waits five years". "He has been waiting (for)five years." OK: He has been sent to prison for ten years, "he waits for five years" and then appeals, protesting his innocence. Under the normal rules he would have been paroled anyway, but because he won't admit his guilt, they keep him in.
How about... "She tells him to wait. He waits five years. She tells him to give up. He waits five years more for her to give up first. She dies. He flies to Russia." Pretty poetic, huh.
This joke telling application of the present simple tense is possible but seems contorted. Perhaps that is not much of a problem for Romance language speakers, who have the tools to sort it out.
But I bet it is precisely for this reason that Duo did not include this sentence in English courses for speakers of languages that have the present simple but lack the present perfect tenses. Users coming from those backgrounds have enough trouble learning the new tenses without us giving them the excuse to cling to what they know and refuse to learn.
I think it is a reasonable observation that the English present historic (which is what I take vivisaurus's example to reflect) would be unlikely to make the cutoff for things sufficiently common and basic to be included in a Duolingo course.
It's not that uncommon. Informal story or joke telling often uses this phrasing. It's also widely used prefixed with "If" - "If he waits one year he'll be old enough to drive", "if you wait a week then you can buy it in the sale".
So, my Portuguese friend has informed my this sentence actually means "He has been waiting five years." Sounds like he wouldn't use "por" here; could be a Brazil/Portugual difference I suppose.