On shabbos we say mekadesh hashabbos.
On yom tov we say mekadesh yisrael vehazemanim.
In other words, we don’t classify shabbos with yom tov. We classify them separately.
Similarly for rosh hashana and for yom kippur. On the former we say mekadesh yisrael veyom hazikaron. On the latter we say mekadesh yisrael veyom hakippurim. Each one is separately classified. They are not classified together with the yamim tovim.
On the other hand, pesach, shavuos, sukos, and shemini atzeres all fall under the rubric of zemanim. We don’t have one mekadesh beracha for pesach and another for shavu-os.
Finally, we have a separate classification for rashei chadashim, where we say mekadesh yisrael verashei chadashim.
This suggests to me that each classification has its own kedusha. The kedusha of yom tov is unlike that of shabbos, and so on. Even when we say mekadesh hashabbos veyisrael vehazemanim, in one bracha, we designate shabbos and zemanim individually, which shows that each has its distinctive nature, its own kind of kedusha. The respective yamim tovim (zemanim), on the other hand, share a common kind of kedusha. This is reflected in the fact that they come under one head in the beracha formulation.
Now let’s view these same barachos from another perspective. On shabbos we say mekadesh hashabbos, in the singular. We don’t say mekadesh shabbasim – this, despite the fact that many shabbasim occur throughout the year. Yet, when it comes to yom tov, we say mekadesh yisrael vehazemanim, in the plural. Presumably this is because there are several yamim tovim in the course of the year. What, then, is the difference?
Ostensibly, the difference is that, although shabbos occurs repeatedly and there are many instances of shabbos in a span of time (e.g., a year), it is the same type of event that repeats itself (as it were). The shabbos of bereishis is of the same genre as the shabbos of no-ach, and so on. By contrast, the yamim tovim that occur through the course of a year are of disparate types: pesach is one event-type, sukos quite another. This, then, is why only one kind of shabbos is mentioned as receiving kedusha (via mekadesh hashabbos, in the singular), while several different kinds of yamim tovim are included in the beracha for the conferral of kedusha on yom tov (via mekadesh hazemanim, in the plural). This reflects the fact that each yom tov is of another type (as a recipient of a general kind of (a zemanimdika) kedusha).
Significantly, though they are themselves of distinctive types, they share in the type of kedusha conferred upon them. That this so is evident from the fact that the beracha, which separates them by using the plural form, also collects them together and heads them under the common epithet zemanim. The intimation being: qua entities, they are indeed individual and separate (several); but as far as their status as bearers of kedusha is concerned they are quite unified and alike. Shabbos, rosh hashana, and yom kippur, on the other hand, are individuated from one another – disparate – both as entities and as bearers of kedusha. This is why they are designated separately – under separate names – in their respective berachos.
But to repeat: shabbos is separate, as an entity and as a recipient of a distinctive kind of kedusha, only in relation to these other events (event-heads). However, individual shabbasim are all alike, both in terms of kedusha and even as entities (thus the singular formulation).
The kedusha of rosh chodesh is of a different kind than that of the yamim tovim or that of shabbos, for example. In its beracha formulation, it is not subsumed any of these others. But unlike the situation with shabbos, its individual occurrences – this month, the next month, the month after, etc – are demarcated separately as types, or event classifications. This is reflected in the use of the plural in the beracha formulation (roshei chadashim). It is not the same entity, receiving repeated instantiations. In this respect, the situation differs from shabbos, whose individual occurrences are deemed of a single type, as reflected in the singular formulation (hashabbos) in the beracha. What makes the individual months separate as entities is an interesting question, but the fact seems undeniable, given the thrust of the foregoing analysis.