There seems to be a grammatical difference of coming in the clouds (not visible to those on the earth) and coming with the clouds or on the clouds (visible to those on the earth). That is, the plain and normal meaning of the prepositions here indicates that being in the clouds is invisible, and being with (or on) the clouds the son of man is visible.
In other words, while the meaning is that Jesus returns to the earth in both cases, his coming in the first case is for his church (in the clouds), and in the latter case to establish his visible theocratic kingdom on earth (with the clouds, or on the clouds).
For example, the references to coming "in the clouds" is restricted to the following passage.
1 Thessalonians 4:17 (NASB)
Then we who are alive and remain will be caught up together with them in the clouds to meet the Lord in the air, and so we shall always be with the Lord.
The meaning of the proposition suggests that this coming of the Lord "in the clouds" will be INVISIBLE to those on the earth. That is, the Lord will take his church from the earth. (Some people call this the "rapture.") People converted to Christianity subsequent to this rapture will still participate in the New Covenant, however they will do so not through the church (body of Jesus Christ) but through the ministration of the faithful remnant of Israel, which will later be "married" to Christ at the wedding supper of the Lamb (Rev 19:9).
In other words, the New Covenant was NEVER PROMISED to Gentiles, but to Israel alone (please compare Jer 31:31 with Heb 8:8). The current time is the "mystery" when Gentiles can participate in the New Covenant only because of their baptism and union with Christ through the Holy Spirit. (Please see Eph 3:4-6.) When the Body of Christ is removed from the earth, the New Covenant will then be in effect on earth only through the faithful ministration of those Israelites who are followers of the Lamb (Rev 14:4). These Israelites sing the song of Moses (Rev 15:3), because they are part of the faithful remnant. The only difference between the Christians of today and Christians in the tribulation are that the former participate in the New Covenant through union with the Body of Christ and the latter through the ministry of the faithful remnant of Israel, to whom the New Covenant was promised...
When the tribulation is completed (approximately seven years), then the Christ will return VISIBLY to the earth, and at that time he will be seen and recognized as the one "who was pierced." In the plain, normal grammatical sense, the following passages identify this second coming as either "on the clouds" Matt 24:30 and Matt 26:64 or "with the clouds": Mark 14:62 and Rev 1:7, which make explicit that this coming will be VISIBLE to the entire earth.