While many answers have been suggested to this question over the years, a simple answer may be that the question is based on textual variants.
The Text of the Haggada
The question is premised on the fact that the text that we have for the wise son's question uses the word אתכם while the text that we have for the wicked son's question uses the word לכם. If both sons used the term "you" instead of "us", why do we only castigate the wicked son and not the wise son? Now while in most texts today this is indeed how the questions appear, this was not always the case. Many old editions of the Haggada (see one of many examples here) have the text of the wise son's question as:
מה העדות והחוקים והמשפטים אשר צוה ה' אלהינו אותנו
That is to say that the word אתכם (you) is replaced with אותנו (us). With this text there is no question; the difference between the wise son and the wicked son is clear – the wicked son excluded himself with the word אתכם while the wise son included himself with the word אותנו.
At the end of Hilchot Chametz U'matza, Rambam provides his version of the Haggada. While the standard text that we have now has the word אתכם in the wise son's question, the Frankel edition notes the existence of editions with the word אותנו:
אתכם. בעץ חיים ובכמה דפו"י אותנו
Other Sources in Rabbinic Literature
The discussion of the four sons appears in external sources (i.e. not the Haggada) as well. In the Mechilta D'Rabbi Yishmael (Parshah 18) the text of the wise son's question reads:
חכם מה הוא אומר מה העדות והחוקים והמשפטים אשר צוה ה' אלהינו אותנו
According to this version, the wise son did not exclude himself, as he in fact asked about the laws that God commanded us.
The text of the wise son's question in the Talmud Yerushalmi (Pesachim 10:4) reads similarly:
בן חכם מהו אומר מה העדות והחקים והמשפטים אשר צוה ה' אלהינו אותנו
Interestingly, in the version recorded in the Midrash Sechel Tov and Midrash Lekach Tov, only the wicked son's question is actually quoted. They don't quote the wise son's question at all. And they have an additional detail not found in the Haggada nor in the Yerushalmi or Mechilta, namely, that they spell out that the problem with the wicked son's question is precisely that he did not use the word לנו.
Midrash Sechel Tov Exodus 13:8
עשה ה' לי. למה נאמר לפי שהוא אומר בבן רשע מה העבודה הזאת לכם ולפי
שהוציא את עצמו מן הכלל שלא אמר לנו בידוע שכפר בעיקר אף אתה הוציאהו
מן הכלל ואומר לו בעבור זה עשה ה' לי ולא לך שאילו הייתה לשם לא הייתה
נגאל פי' אלא כבר היית מת בשלשת ימי אפילה
Midrash Lekach Tov Exodus 13:8
רשע מה הוא אומר מה העבודה הזאת לכם כלומר לכם ולא לו ולפי שהוציא את
עצמו מן הכלל שלא אמר לנו אלא לכם בידוע שכפר בעיקר לכך נאמר בעבור זה
עשה ה' לי כלומר לי ולא לו שאלו היה שם לא היה נגאל אלא היה מת בשלשת ימי
According to this version, almost all the other suggested answers are eliminated, as they rely on using some other aspect of the wicked son's question to explain why it is problematic, yet here we are specifically told that the problematic aspect is his failure to include himself. Thus, virtually the only way to explain why we are okay with the wise son's question would be to say that he did not in fact say אתכם.
The Scriptural Source
While to resolve the discrepancy between the way we treat the wise and wicked sons we can suggest that the correct version of the wise son's question did not contain the word אתכם, (rather it has אותנו) it leaves us with a very basic problem. The questions of the four sons are derived from Scripture. The question of the wise son is taken from Deuteronomy 6:20 which reads as follows:
כִּי יִשְׁאָלְךָ בִנְךָ מָחָר לֵאמֹר מָה הָעֵדֹת וְהַחֻקִּים
וְהַמִּשְׁפָּטִים אֲשֶׁר צִוָּה יְהוָה אֱלֹהֵינוּ אֶתְכֶם
When thy son asketh thee in time to come, saying: 'What mean the
testimonies, and the statutes, and the ordinances, which the LORD our
God hath commanded you? (Mechon Mamre translation)
As we see clearly in the Scriptural verse, the question of the wise son does in fact contain the word אתכם. How does this square with all the sources that have the word אותנו?
The Penei Moshe
This problem is dealt with by R. Moshe Margoliot in his commentary (Penei Moshe) to the passage in the Talmud Yerushalmi. He suggests that although the text in the Torah has the word אתכם, the wise son deliberately changed it and used the word אותנו precisely to avoid excluding himself:
ובכתוב נאמר אשר צוה ה' אלהינו אתכם אלא שהחכם ניכר בשאלתו ואינו רוצה
לומר אתכם ואומר אותנו שלא להוציא עצמו מן הכלל
According to this, the wise son is indeed distinguished from the wicked son, and we do not reject him precisely because he included himself by saying אותנו.
The Septuagint and Vulgate
We can actually go one step further than R. Margoliot's answer. If we look at the ancient Greek and Latin translations of the Torah, the Septuagint and the Vulgate, we find that they translate the last word of Deuteronomy 6:20 as "us" and not "you". This might indicate that there was even a version of the Torah that had the word as אותנו in the wise son's question.
καὶ ἔσται ὅταν ἐρωτήσῃ σε ὁ υἱός σου αὔριον λέγων τί ἐστιν τὰ μαρτύρια
καὶ τὰ δικαιώματα καὶ τὰ κρίματα ὅσα ἐνετείλατο κύριος ὁ θεὸς ἡμῶν
And it shall come to pass when thy son shall ask thee at a future
time, saying, What are the testimonies, and the ordinances, and the
judgments, which the Lord our God has commanded us? (Brenton
cum interrogaverit te filius tuus cras dicens quid sibi volunt testimonia haec et caerimoniae atque iudicia quae praecepit Dominus
Deus noster nobis
And when thy son shall ask thee to morrow, saying: What mean these
testimonies, and ceremonies and judgments, which the Lord our God hath
commanded us? (Translation)
This is particularly noteworthy because (some versions of) the Mechilta cited above did not just have the word אותנו in the wise son's question; it also has the word אותנו in the quotation of the verse at the beginning of the exposition, perhaps again indicating the existence of a variant text in the Torah.
If even the text of the Torah itself said אותנו by the wise son, the question would surely fall by the wayside.
Interestingly, Rabbi Dr. Professor Allen Schwartz noted the fact that the other sources (Mechilta, Yerushalmi, and Septuagint) have the word as אותנו, but he explained it in reverse. He suggested that this is further evidence of the earliness of the Haggada, and that in fact the Mechilta, Yerushalmi, and Septuagint were all influenced by the Haggada. That is to say, that all three of these other sources deliberately changed the text from how it was in the Haggada (replacing אתכם with אותנו) precisely to avoid the question of how we differentiate the wise son from the wicked son. (This is in fact similar to the answer given by R. Margoliot mentioned above.) This suggestion, as well as his broader discussion of this question, can be found in this lecture.