Chazal instituted that we drink four cups of wine on Pesach night.
The first cup of wine is that of Kadeish. In other words, the first cup of wine we would be drinking anyway to fulfill the normal obligation of Kiddush. Further, if Pesach falls out on Motza'ei Shabbos, this cup is also used for havdalah. During the seder there are mulitple obligations that involve a cup of wine. Why only four cups instead of giving each obligation its own separate cup of wine?
Depending on what you hold about kos shel brachah, perhaps the same question would apply to the third cup.
This question would also apply to any Yom Tov that falls out on Motzaei Shabbos, where Kiddush and Havdalah use the same cup.
(In comparison, if a person has two chiyuvim to bring karbanos, he can't fulfill them with the same animal.)
Possibly relevant is the discussion in Pesachim 115a regarding mitzvos mevatlos zu es zu. Also possibly relevant is the discussion in this question and this one regarding whether the daled kosos are one mitzvah or four separate ones.