In Parshas Haazinu (32:7) we are told:
זְכֹר יְמוֹת עוֹלָם בִּינוּ שְׁנוֹת דּוֹר־וָדוֹר שְׁאַל אָבִיךָ וְיַגֵּדְךָ זְקֵנֶיךָ וְיֹאמְרוּ לָךְ׃
Remember the days of old consider the years of many generations: ask thy father, and he will recount it to thee; thy elders, and they will tell thee.
It is a direct instruction, using the imperative command ‘Zechor!’ Why isn’t this counted as a mitzvah?
You are of course correct that the classical monei hamitzvot do not count zekhor yemot olam as one of the 613 mitzvot.
However, it is worth noting the words of R. Tazdok HaKohen of Lublin in his Sefer HaZikhronot, mitzvah 3 (printed as an appendix to Divrei Soferim):
ויראה שמאמר זכור ימות וגו' שבא בלשון ציווי יהי' מצוה מיוחדת על הענין הזה להתבונן בחסדי הש"י עמנו וימות עולם ובכל דור ודור
It would appear that the words "zekhor yemot olam etc." which are written in the imperative tense, are their own mitzvah regarding this matter, to contemplate G-d's kindnesses to us throughout history.
So why (classically) was this not considered a mitzvah?
I would argue that in the world of Rambam and Ramban, there can be no such thing as a formal mitzvah to simply remember something. If there is a mitzvah which seems to be telling us to remember something, they will only include it in their counts if it actually also involves a requirement to speak.
Thus, for Rambam, Shemot 13:3 (the Exodus), Shemot 20:8 (shabbat) and Devarim 25:17 (Amalek) are all understood (following Chazal) to be mandating speech, not mere memory; see Sefer HaMitzvot, mitzvot aseh 157, 155 and 189 respectively.
(See also Peri Megadim in his introduction to Hilkhot Keriat Shema, who suggests that Rambam will not count a mitzvah which involves mere zekhirah belev (mentally remembering), although he concedes that this argument requires further thought.)
Even Ramban, who wants to add more "memory mitzvot" to the list, will only do so if he can find a mandate to speak. Thus Devarim 4:9-10 (giving of the Torah at Sinai) is a mandate to pass on that memory to one's descendants (והודעתם לבניך ולבני בניך) (Shikhchat HaLavin 2).
Even more strikingly, for Ramban to add Devarim 24:9 (Miriam) and Devarim 9:7 (the sins in the desert) to the list, he needs to rely on a midrash (Sifra Bechukotai 26:3) which mandates that one speaks about these matters (Shikhchat Ha-Asin 7).
Given that we have no source in Chazal which understands zechor yemot olam as requiring us to say something, we can understand that for Rambam and Ramban it doesn't merit inclusion in the count of the 613 mitzvot.
(Why don't Chazal understand zekhor yemot olam to mandate speaking? If you look at the above-referenced midrash, you'll see that they only do so if they can find another verse requiring merely remembering that subject, thus making the "zakhor" verses redundant, unless we understand them to be requiring speech in addition to memory. Zekhor yemot olam has no such second verse available, thus it is presumably referring to memory alone, and not to speech.)
