Many of your point are only relevant to Modern Hebrew, which is a distinct language from Biblical Hebrew, only the latter being a holy language. In fact, many orthodox Jews distance themselves from Modern Hebrew (to the point of prohibiting its use in their synagogues) because of what is deemed to be its inherent un-holiness.
Nevertheless, let me address each of your points separately:
- There are multiple letters for the same sound (sin and samech, vav and bet, tet and taf).
In fact, each letter used to have a distinct sound, but over the course of history, much of such distinction has been lost. The best preserving dialect of Hebrew is probably the Yemenite, where there is a clear distinction between waw/veth and dteth/taw. I even heard from an authentic Yemenite source that in some Yemenite villages a distinction between sin and samach remains, the latter being about half-way between sin and tsadi.
- There are multiple sounds for the same letter (vav can be an u, an o or a v).
Some letters have subdivisions (shin and sin, bet and vet, etc).
This could be in explained in many ways. Here is a simplified Kabbalistic explanation: God created the world through the 10 vowels and 22 letters. Each represents fundamental concepts and their connections. Each word consists of a collection of such concepts and connections that together form the meaning of the word. (E.g. Av = Alef + Beth = Master + House = Master of the house.) Some letters need to show different aspects of themselves to correctly bring out the meaning.
- Just five letters have a sofit version.
According to the first opinion in Sanhedrin (as it happens, this is the view held by archaeologists too), the Torah was originally in Ksav Ivri which does not have these forms. In the time of Ezra, the original script was replaced by Ksav Ashuris which has these alternate forms. A further indication of this is that Sefer Yetzira (by Avraham Avinu) never mentions the final forms.
- Two nikkudot can have totally different sounds but be written exactly identical (such as kamatz, that can be an a or an o).
This is not an anomaly. Just as with the letters, each vowel also variants. Most have two length-variants. (E.g. Chataf segol/Segol, Chirik katan/Chirik gadol, Shva nach/Shva na') Again, the distinction between many such pairs have been lost by various groups, and mostly preserved by the Yemenites.
- Many sounds aren't in the Hebrew alphabet (like g in george, ch in change, etc).
No language contains all sounds made by man. However, the ones included in Hebrew are the ones that were fundamental to the Creation. One could argue that all other sounds a made up of combinations of the 32 (including their variations) that we have. (E.g. George = D + Z + Sh, Change = T + Sh.)